doc/.site
doc/sdk/python/arvados
doc/sdk/R/arvados
+doc/sdk/java-v2/javadoc
sdk/perl/MYMETA.*
sdk/perl/Makefile
sdk/perl/blib
*.Rd
lib/dispatchcloud/test/sshkey_*
*.asc
+sdk/java-v2/build.gradle
+sdk/java-v2/settings.gradle
# NOTE: This requires GNU getopt (part of the util-linux package on Debian-based distros).
TEMP=`getopt -o hut:r: \
- --long help,upload,no-cache,tags,repo: \
+ --long help,upload,no-cache,tags:,repo: \
-n "$0" -- "$@"`
if [ $? != 0 ] ; then echo "Use -h for help"; exit 1 ; fi
sdk/go/crunchrunner
sdk/cwl
sdk/R
+sdk/java-v2
tools/sync-groups
tools/crunchstat-summary
tools/crunchstat-summary:py3
services/fuse
services/nodemanager
tools/crunchstat-summary
+ tools/crunchstat-summary:py3
)
declare -a gostuff
&& KEEP_LOCAL_STORE=/tmp/keep bundle exec rake test TESTOPTS=-v ${testargs[sdk/cli]}
}
+test_sdk/java-v2() {
+ cd "$WORKSPACE/sdk/java-v2" && gradle test
+}
+
test_services/login-sync() {
cd "$WORKSPACE/services/login-sync" \
&& bundle exec rake test TESTOPTS=-v ${testargs[services/login-sync]}
do_test sdk/R
do_test sdk/cli
do_test services/login-sync
+ do_test sdk/java-v2
do_test services/nodemanager_integration
for p in "${pythonstuff[@]}"
do
require "rubygems"
require "colorize"
-task :generate => [ :realclean, 'sdk/python/arvados/index.html', 'sdk/R/arvados/index.html' ] do
+#task :generate => [ :realclean, 'sdk/python/arvados/index.html', 'sdk/R/arvados/index.html', 'sdk/java-v2/javadoc/index.html' ] do
+task :generate => [ :realclean, 'sdk/python/arvados/index.html', 'sdk/java-v2/javadoc/index.html' ] do
vars = ['baseurl', 'arvados_cluster_uuid', 'arvados_api_host', 'arvados_workbench_host']
vars.each do |v|
if ENV[v]
end
end
+file "sdk/java-v2/javadoc/index.html" do |t|
+ `which java`
+ if $? == 0
+ `which gradle`
+ if $? != 0
+ puts "Warning: gradle not found, java sdk documentation will not be generated".colorize(:light_red)
+ else
+ tgt = Dir.pwd
+ docfiles = []
+ Dir.chdir("../sdk/java-v2") do
+ STDERR.puts `gradle javadoc 2>&1`
+ raise if $? != 0
+ end
+ cp_r("../sdk/java-v2/build/docs/javadoc", "sdk/java-v2")
+ raise if $? != 0
+ end
+ else
+ puts "Warning: java not found, java sdk documentation will not be generated".colorize(:light_red)
+ end
+end
+
task :linkchecker => [ :generate ] do
Dir.chdir(".site") do
`which linkchecker`
task :clean do
rm_rf "sdk/python/arvados"
rm_rf "sdk/R"
+ rm_rf "sdk/java-v2/javadoc"
end
require "zenweb/tasks"
- Ruby:
- sdk/ruby/index.html.textile.liquid
- sdk/ruby/example.html.textile.liquid
- - Java:
+ - Java v2:
+ - sdk/java-v2/index.html.textile.liquid
+ - sdk/java-v2/example.html.textile.liquid
+ - sdk/java-v2/javadoc.html.textile.liquid
+ - Java v1:
- sdk/java/index.html.textile.liquid
- sdk/java/example.html.textile.liquid
api:
AuthToken: zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
KeepServiceTypes:
- disk
-Listen: :9005
ManagementToken: <span class="userinput">xyzzy</span>
RunPeriod: 10m
CollectionBatchSize: 100000
CollectionBuffers: 1000
+LostBlocksFile: /tmp/keep-balance-lost-blocks.txt # If given, this file will be updated atomically during each successful run.
</code></pre>
</notextile>
* "R SDK":{{site.baseurl}}/sdk/R/index.html
* "Perl SDK":{{site.baseurl}}/sdk/perl/index.html
* "Ruby SDK":{{site.baseurl}}/sdk/ruby/index.html
-* "Java SDK":{{site.baseurl}}/sdk/java/index.html
+* "Java SDK v2":{{site.baseurl}}/sdk/java-v2/index.html
+* "Java SDK v1":{{site.baseurl}}/sdk/java/index.html
Many Arvados Workbench pages, under the the *Advanced* tab, provide examples of API and SDK use for accessing the current resource .
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Java SDK v2
+title: Examples
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+In these examples, the site prefix is @aaaaa@.
+
+h2. Initialize SDK
+
+{% codeblock as java %}
+package org.arvados.example;
+
+import java.util.List;
+import org.arvados.client.config.ConfigProvider;
+import org.arvados.client.config.ExternalConfigProvider;
+import org.arvados.client.api.model.CollectionList;
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.api.client.CollectionsApiClient;
+
+public class CollectionExample {
+ public static void main(String[] argv) {
+ ConfigProvider conf = ExternalConfigProvider.builder().
+ apiProtocol("https").
+ apiHost("qr1hi.arvadosapi.com").
+ apiPort(443).
+ apiToken("...").
+ build();
+ CollectionsApiClient collectionsApi = new CollectionsApiClient(conf);
+ /* ... */
+ }
+}
+{% endcodeblock %}
+
+h2. list
+
+{% codeblock as java %}
+ CollectionList cl = collectionsApi.list();
+ List<Collection> items = cl.getItems();
+ for (int i = 0; i < items.size(); i++) {
+ System.out.println(items.get(i));
+ }
+{% endcodeblock %}
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Java SDK v2
+title: "Installation"
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+The Arvados Java SDK v2 provides a high level API for working with Arvados resources.
+
+h2. Using the SDK
+
+The SDK is packaged as a JAR named @arvados-java-<version>.jar@, which is published to Maven Central and can be included using Maven, Gradle, or by hand.
+
+Here is an example @build.gradle@ file that uses the Arados java sdk:
+
+<pre>
+apply plugin: 'application'
+apply plugin: 'java-library'
+apply plugin: 'maven'
+
+repositories {
+ mavenCentral()
+}
+
+application {
+ mainClassName = "org.arvados.example.CollectionExample"
+}
+
+dependencies {
+ api 'org.arvados:arvados-java-sdk:0.1.0'
+}
+</pre>
+
+See "Java SDK Examples":example.html to get started using the SDK.
+
+h3. Logging
+
+The SDK uses the SLF4J facade library for logging. A concrete logging "binding":https://www.slf4j.org/manual.html#swapping (and configuration, if required) must be provided by a client. For small applications, you can use the Simple implementation by adding slf4j-simple-1.8.0-beta4.jar to your classpath.
+
+h3. Configuration
+
+"TypeSafe Configuration":https://github.com/lightbend/config is used for configuring this library.
+
+Please review src/main/resources/reference.conf for default values provided with this library.
+
+* **keepweb-host** - host of your Keep-Web server (default: localhost)
+* **keepweb-port** - port of your Keep-Web server (default: 8000)
+* **host** - host of your Arvados API server
+* **port** - port of your Arvados API server
+* **token** - Arvados token to authenticate registered user, one must provide "token obtained from Arvados Workbench":https://doc.arvados.org/user/reference/api-tokens.html
+* **protocol** - don't change to unless really needed (default: https)
+* **host-insecure** - ignores SSL certificate verification if true (default: false Don't change to *true* unless really needed)
+* **split-size** - size of chunk files in megabytes (default: 64)
+* **temp-dir** - temporary chunk files storage
+* **copies** - amount of chunk files duplicates per Keep server
+* **retries** - UNIMPLEMENTED
+
+In order to override default settings one can create an application.conf file in an application. Example: src/test/resources/application.conf.
+
+Alternatively @ExternalConfigProvider@ class can be used to pass configuration via code. @ExternalConfigProvider@ comes with a builder and all of the above values must be provided in order for it to work properly.
+
+@ArvadosFacade@ has two constructors, one without arguments that uses values from application.conf and second one taking @ExternalConfigProvider@ as an argument.
+
+h3. API clients
+
+All API clients inherit from @BaseStandardApiClient@. This class contains implementation of all common methods as described in "Arvados Common Resource Methods":http://doc.arvados.org/api/methods.html.
+
+Parameters provided to common or specific methods are String UUID or fields wrapped in Java objects. For example:
+
+{% codeblock as java %}
+String uuid = "ardev-4zz18-rxcql7qwyakg1r1";
+
+Collection actual = client.get(uuid);
+{% endcodeblock %}
+
+{% codeblock as java %}
+ListArgument listArgument = ListArgument.builder()
+ .filters(Arrays.asList(
+ Filter.of("owner_uuid", Operator.LIKE, "ardev%"),
+ Filter.of("name", Operator.LIKE, "Super%"),
+ Filter.of("portable_data_hash", Operator.IN, Lists.newArrayList("54f6d9f59065d3c009d4306660989379+65")
+ )))
+ .build();
+
+CollectionList actual = client.list(listArgument);
+{% endcodeblock %}
+
+Non-standard API clients must inherit from BaseApiClient. For example: KeepServerApiClient communicates directly with Keep servers using exclusively non-common methods.
+
+h3. Business logic
+
+More advanced API data handling could be implemented as *Facade* classes. In current version functionalities provided by SDK are handled by @ArvadosFacade@. They include:
+
+* **downloading single file from collection** - using Keep-Web
+* **downloading whole collection** - using Keep-Web or Keep Server API
+* **listing file info from certain collection** - information is returned as list of *FileTokens* providing file details
+* **uploading single file** - to either new or existing collection
+* **uploading list of files** - to either new or existing collection
+* **creating an empty collection**
+* **getting current user info**
+* **listing current user's collections**
+* **creating new project**
+* **deleting certain collection**
+
+h3. Note regarding Keep-Web
+
+The Java SDK requires Keep Web (which is part of the standard configuration) as well as the API server and Keep server(s).
+
+h3. Integration tests
+
+In order to run the integration tests, all fields within following configuration file must be provided: @src/test/resources/integration-test-appliation.conf@
+
+
+The parameter @integration-tests.project-uuid@ should contain UUID of one project available to user who's token was provided within configuration file.
+
+Integration tests require connection to a real Arvados server.
+
+h3. Note regarding file naming
+
+When uploading via the current implementation of the Java SDK all uploaded files within single collection must have different names. This applies also to uploading files to already existing collection. Renaming files with duplicate names is not currently implemented.
+
+h3. Javadoc
+
+See "Javadoc":javadoc.html
+
+h2. Building the Arvados SDK
+
+Dependencies:
+* JDK for Java 8 or later "https://www.oracle.com/technetwork/java/javase/downloads/index.html":https://www.oracle.com/technetwork/java/javase/downloads/index.html
+* Gradle "https://gradle.org/install/":https://gradle.org/install/
+
+
+<notextile>
+<pre>
+$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">cd arvados/sdk/java-v2</code>
+$ <code class="userinput">gradle test</code>
+$ <code class="userinput">gradle jar</code>
+</pre>
+This will build the SDK and run all unit tests, then generate an Arvados Java sdk jar file in build/libs/arvados-java-2.0.0.jar
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Java v2
+title: "Javadoc Reference"
+
+no_nav_left: true
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+notextile. <iframe src="javadoc/index.html" style="width:100%; height:100%; border:none" />
---
layout: default
navsection: sdk
-navmenu: Java
+navmenu: Java SDK v1
title: "Installation"
...
{% comment %}
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The Java SDK provides a generic set of wrappers so you can make API calls in java.
+The Java SDK v1 provides a low level API to call Arvados from Java.
h3. Introdution
--- /dev/null
+/.gradle/
+/bin/
+/build/
+.project
+.classpath
+/.settings/
+.DS_Store
+/.idea/
+/out/
--- /dev/null
+.licenseignore
+agpl-3.0.txt
+apache-2.0.txt
+COPYING
\ No newline at end of file
--- /dev/null
+Unless indicated otherwise in the header of the file, the files in this
+repository are dual-licensed AGPL-3.0 and Apache-2.0
+
+Individual files contain an SPDX tag that indicates the license for the file.
+dual-licensed files use the following tag:
+
+ SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+
+This enables machine processing of license information based on the SPDX
+License Identifiers that are available here: http://spdx.org/licenses/
+
+The full license text for each license is available in this directory:
+
+ AGPL-3.0: agpl-3.0.txt
+ Apache-2.0: apache-2.0.txt
--- /dev/null
+```
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+```
+
+# Arvados Java SDK
+
+##### About
+Arvados Java Client allows to access Arvados servers and uses two APIs:
+* lower level [Keep Server API](https://doc.arvados.org/api/index.html)
+* higher level [Keep-Web API](https://godoc.org/github.com/curoverse/arvados/services/keep-web) (when needed)
+
+##### Required Java version
+This SDK requires Java 8+
+
+##### Logging
+
+SLF4J is used for logging. Concrete logging framework and configuration must be provided by a client.
+
+##### Configuration
+
+[TypeSafe Configuration](https://github.com/lightbend/config) is used for configuring this library.
+
+Please, have a look at java/resources/reference.conf for default values provided with this library.
+
+* **keepweb-host** - change to host of your Keep-Web installation
+* **keepweb-port** - change to port of your Keep-Web installation
+* **host** - change to host of your Arvados installation
+* **port** - change to port of your Arvados installation
+* **token** - authenticates registered user, one must provide
+ [token obtained from Arvados Workbench](https://doc.arvados.org/user/reference/api-tokens.html)
+* **protocol** - don't change to unless really needed
+* **host-insecure** - insecure communication with Arvados (ignores SSL certificate verification),
+ don't change to *true* unless really needed
+* **split-size** - size of chunk files in megabytes
+* **temp-dir** - temporary chunk files storage
+* **copies** - amount of chunk files duplicates per Keep server
+* **retries** - in case of chunk files send failure this should allow to repeat send
+ (*NOTE*: this parameter is not used at the moment but was left for future improvements)
+
+In order to override default settings one can create application.conf file in an application.
+Example: src/test/resources/application.conf.
+
+Alternatively ExternalConfigProvider class can be used to pass configuration via code.
+ExternalConfigProvider comes with a builder and all of the above values must be provided in order for it to work properly.
+
+ArvadosFacade has two constructors, one without arguments that uses values from reference.conf and second one
+taking ExternalConfigProvider as an argument.
+
+##### API clients
+
+All API clients inherit from BaseStandardApiClient. This class contains implementation of all
+common methods as described in http://doc.arvados.org/api/methods.html.
+
+Parameters provided to common or specific methods are String UUID or fields wrapped in Java objects. For example:
+
+```java
+String uuid = "ardev-4zz18-rxcql7qwyakg1r1";
+
+Collection actual = client.get(uuid);
+```
+
+```java
+ListArgument listArgument = ListArgument.builder()
+ .filters(Arrays.asList(
+ Filter.of("owner_uuid", Operator.LIKE, "ardev%"),
+ Filter.of("name", Operator.LIKE, "Super%"),
+ Filter.of("portable_data_hash", Operator.IN, Lists.newArrayList("54f6d9f59065d3c009d4306660989379+65")
+ )))
+ .build();
+
+CollectionList actual = client.list(listArgument);
+```
+
+Non-standard API clients must inherit from BaseApiClient.
+For example: KeepServerApiClient communicates directly with Keep servers using exclusively non-common methods.
+
+##### Business logic
+
+More advanced API data handling could be implemented as *Facade* classes.
+In current version functionalities provided by SDK are handled by *ArvadosFacade*.
+They include:
+* **downloading single file from collection** - using Keep-Web
+* **downloading whole collection** - using Keep-Web or Keep Server API
+* **listing file info from certain collection** - information is returned as list of *FileTokens* providing file details
+* **uploading single file** - to either new or existing collection
+* **uploading list of files** - to either new or existing collection
+* **creating an empty collection**
+* **getting current user info**
+* **listing current user's collections**
+* **creating new project**
+* **deleting certain collection**
+
+##### Note regarding Keep-Web
+
+Current version requires both Keep Web and standard Keep Server API configured in order to use Keep-Web functionalities.
+
+##### Integration tests
+
+In order to run integration tests all fields within following configuration file must be provided:
+```java
+src/test/resources/integration-test-appliation.conf
+```
+Parameter **integration-tests.project-uuid** should contain UUID of one project available to user,
+whose token was provided within configuration file.
+
+Integration tests require connection to real Arvados server.
+
+##### Note regarding file naming
+
+While uploading via this SDK all uploaded files within single collection must have different names.
+This applies also to uploading files to already existing collection.
+Renaming files with duplicate names is not implemented in current version.
+
--- /dev/null
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+our General Public Licenses are intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+ Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
+
+ A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate. Many developers of free software are heartened and
+encouraged by the resulting cooperation. However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
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+
+ The GNU Affero General Public License is designed specifically to
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+users of that server. Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
+
+ An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals. This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing under
+this license.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
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+
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+
+ "This License" refers to version 3 of the GNU Affero General Public License.
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+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
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+ The Corresponding Source need not include anything that users
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+ The Corresponding Source for a work in source code form is that
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+ 2. Basic Permissions.
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+ All rights granted under this License are granted for the term of
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+ 14. Revised Versions of this License.
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+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
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+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
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+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
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+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
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+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<http://www.gnu.org/licenses/>.
--- /dev/null
+
+ Apache License
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+ http://www.apache.org/licenses/
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+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
--- /dev/null
+apply plugin: 'java-library'
+apply plugin: 'eclipse'
+apply plugin: 'idea'
+apply plugin: 'maven'
+apply plugin: 'signing'
+
+
+repositories {
+ mavenCentral()
+}
+
+dependencies {
+ api 'com.squareup.okhttp3:okhttp:3.9.1'
+ api 'com.fasterxml.jackson.core:jackson-databind:2.9.2'
+ api 'com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.9.2'
+ api 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.9.2'
+ api 'commons-codec:commons-codec:1.11'
+ api 'commons-io:commons-io:2.6'
+ api 'com.google.guava:guava:23.4-jre'
+ api 'org.slf4j:slf4j-api:1.7.25'
+ api 'com.typesafe:config:1.3.2'
+
+ testImplementation 'junit:junit:4.12'
+ testImplementation 'org.mockito:mockito-core:2.12.0'
+ testImplementation 'org.assertj:assertj-core:3.8.0'
+ testImplementation 'com.squareup.okhttp3:mockwebserver:3.9.1'
+}
+
+test {
+ useJUnit {
+ excludeCategories 'org.arvados.client.junit.categories.IntegrationTests'
+ }
+
+ testLogging {
+ events "passed", "skipped", "failed"
+ afterSuite { desc, result ->
+ if (!desc.parent) { // will match the outermost suite
+ println "\n---- Test results ----"
+ println "${result.resultType} (${result.testCount} tests, ${result.successfulTestCount} successes, ${result.failedTestCount} failures, ${result.skippedTestCount} skipped)"
+ println ""
+ }
+ }
+ }
+}
+
+task integrationTest(type: Test) {
+ useJUnit {
+ includeCategories 'org.arvados.client.junit.categories.IntegrationTests'
+ }
+}
+
+task javadocJar(type: Jar) {
+ classifier = 'javadoc'
+ from javadoc
+}
+
+task sourcesJar(type: Jar) {
+ classifier = 'sources'
+ from sourceSets.main.allSource
+}
+
+artifacts {
+ archives javadocJar, sourcesJar
+}
+
+signing {
+ sign configurations.archives
+}
+
+uploadArchives {
+ repositories {
+ mavenDeployer {
+ beforeDeployment { MavenDeployment deployment -> signing.signPom(deployment) }
+
+ repository(url: "https://oss.sonatype.org/service/local/staging/deploy/maven2") {
+ authentication(userName: ossrhUsername, password: ossrhPassword)
+ }
+
+ snapshotRepository(url: "https://oss.sonatype.org/content/repositories/snapshots") {
+ authentication(userName: ossrhUsername, password: ossrhPassword)
+ }
+
+ pom.project {
+ name 'Arvados Java SDK'
+ packaging 'jar'
+ groupId 'org.arvados'
+ description 'Arvados Java SDK'
+ url 'https://github.com/curoverse/arvados'
+
+ scm {
+ url 'scm:git@https://github.com/curoverse/arvados.git'
+ connection 'scm:git@https://github.com/curoverse/arvados.git'
+ developerConnection 'scm:git@https://github.com/curoverse/arvados.git'
+ }
+
+ licenses {
+ license {
+ name 'The Apache License, Version 2.0'
+ url 'http://www.apache.org/licenses/LICENSE-2.0.txt'
+ }
+ }
+
+ developers {
+ developer {
+ id 'veritasgenetics'
+ name 'Veritas Genetics'
+ email 'ops@veritasgenetics.com'
+ }
+ }
+ }
+ }
+ }
+}
--- /dev/null
+/*
+ Copyright (C) The Arvados Authors. All rights reserved.
+
+ SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+*/
+
+ossrhUsername = ''
+ossrhPassword = ''
--- /dev/null
+rootProject.name = 'arvados-java-sdk'
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.arvados.client.exception.ArvadosApiException;
+import org.arvados.client.api.client.factory.OkHttpClientFactory;
+import org.arvados.client.api.model.ApiError;
+import org.arvados.client.config.ConfigProvider;
+import okhttp3.OkHttpClient;
+import okhttp3.Request;
+import okhttp3.Response;
+import okhttp3.ResponseBody;
+import org.slf4j.Logger;
+
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
+import java.util.Objects;
+
+abstract class BaseApiClient {
+
+ static final ObjectMapper MAPPER = new ObjectMapper().findAndRegisterModules();
+
+ final OkHttpClient client;
+ final ConfigProvider config;
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(BaseApiClient.class);
+
+ BaseApiClient(ConfigProvider config) {
+ this.config = config;
+ client = OkHttpClientFactory.builder()
+ .build()
+ .create(config.isApiHostInsecure());
+ }
+
+ Request.Builder getRequestBuilder() {
+ return new Request.Builder()
+ .addHeader("authorization", String.format("OAuth2 %s", config.getApiToken()))
+ .addHeader("cache-control", "no-cache");
+ }
+
+ String newCall(Request request) {
+ return (String) getResponseBody(request, body -> body.string().trim());
+ }
+
+ byte[] newFileCall(Request request) {
+ return (byte[]) getResponseBody(request, ResponseBody::bytes);
+ }
+
+ private Object getResponseBody(Request request, Command command) {
+ try {
+ log.debug(URLDecoder.decode(request.toString(), StandardCharsets.UTF_8.name()));
+ } catch (UnsupportedEncodingException e) {
+ throw new ArvadosApiException(e);
+ }
+
+ try (Response response = client.newCall(request).execute()) {
+ ResponseBody responseBody = response.body();
+
+ if (!response.isSuccessful()) {
+ String errorBody = Objects.requireNonNull(responseBody).string();
+ if (errorBody == null || errorBody.length() == 0) {
+ throw new ArvadosApiException(String.format("Error code %s with message: %s", response.code(), response.message()));
+ }
+ ApiError apiError = MAPPER.readValue(errorBody, ApiError.class);
+ throw new ArvadosApiException(String.format("Error code %s with messages: %s", response.code(), apiError.getErrors()));
+ }
+ return command.readResponseBody(responseBody);
+ } catch (IOException e) {
+ throw new ArvadosApiException(e);
+ }
+ }
+
+ private interface Command {
+ Object readResponseBody(ResponseBody body) throws IOException;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectWriter;
+import okhttp3.MediaType;
+import okhttp3.HttpUrl;
+import okhttp3.HttpUrl.Builder;
+import okhttp3.Request;
+import okhttp3.RequestBody;
+import org.arvados.client.exception.ArvadosApiException;
+import org.arvados.client.api.model.Item;
+import org.arvados.client.api.model.ItemList;
+import org.arvados.client.api.model.argument.ListArgument;
+import org.arvados.client.config.ConfigProvider;
+import org.slf4j.Logger;
+
+import java.io.IOException;
+import java.util.Map;
+
+public abstract class BaseStandardApiClient<T extends Item, L extends ItemList> extends BaseApiClient {
+
+ private static final MediaType JSON = MediaType.parse(com.google.common.net.MediaType.JSON_UTF_8.toString());
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(BaseStandardApiClient.class);
+
+ BaseStandardApiClient(ConfigProvider config) {
+ super(config);
+ }
+
+ public L list(ListArgument listArguments) {
+ log.debug("Get list of {}", getType().getSimpleName());
+ Builder urlBuilder = getUrlBuilder();
+ addQueryParameters(urlBuilder, listArguments);
+ HttpUrl url = urlBuilder.build();
+ Request request = getRequestBuilder().url(url).build();
+ return callForList(request);
+ }
+
+ public L list() {
+ return list(ListArgument.builder().build());
+ }
+
+ public T get(String uuid) {
+ log.debug("Get {} by UUID {}", getType().getSimpleName(), uuid);
+ HttpUrl url = getUrlBuilder().addPathSegment(uuid).build();
+ Request request = getRequestBuilder().get().url(url).build();
+ return callForType(request);
+ }
+
+ public T create(T type) {
+ log.debug("Create {}", getType().getSimpleName());
+ String json = mapToJson(type);
+ RequestBody body = RequestBody.create(JSON, json);
+ Request request = getRequestBuilder().post(body).build();
+ return callForType(request);
+ }
+
+ public T delete(String uuid) {
+ log.debug("Delete {} by UUID {}", getType().getSimpleName(), uuid);
+ HttpUrl url = getUrlBuilder().addPathSegment(uuid).build();
+ Request request = getRequestBuilder().delete().url(url).build();
+ return callForType(request);
+ }
+
+ public T update(T type) {
+ String uuid = type.getUuid();
+ log.debug("Update {} by UUID {}", getType().getSimpleName(), uuid);
+ String json = mapToJson(type);
+ RequestBody body = RequestBody.create(JSON, json);
+ HttpUrl url = getUrlBuilder().addPathSegment(uuid).build();
+ Request request = getRequestBuilder().put(body).url(url).build();
+ return callForType(request);
+ }
+
+ @Override
+ Request.Builder getRequestBuilder() {
+ return super.getRequestBuilder().url(getUrlBuilder().build());
+ }
+
+ HttpUrl.Builder getUrlBuilder() {
+ return new HttpUrl.Builder()
+ .scheme(config.getApiProtocol())
+ .host(config.getApiHost())
+ .port(config.getApiPort())
+ .addPathSegment("arvados")
+ .addPathSegment("v1")
+ .addPathSegment(getResource());
+ }
+
+ <TL> TL call(Request request, Class<TL> cls) {
+ String bodyAsString = newCall(request);
+ try {
+ return mapToObject(bodyAsString, cls);
+ } catch (IOException e) {
+ throw new ArvadosApiException("A problem occurred while parsing JSON data", e);
+ }
+ }
+
+ private <TL> TL mapToObject(String content, Class<TL> cls) throws IOException {
+ return MAPPER.readValue(content, cls);
+ }
+
+ private <TL> String mapToJson(TL type) {
+ ObjectWriter writer = MAPPER.writer().withDefaultPrettyPrinter();
+ try {
+ return writer.writeValueAsString(type);
+ } catch (JsonProcessingException e) {
+ log.error(e.getMessage());
+ return null;
+ }
+ }
+
+ T callForType(Request request) {
+ return call(request, getType());
+ }
+
+ L callForList(Request request) {
+ return call(request, getListType());
+ }
+
+ abstract String getResource();
+
+ abstract Class<T> getType();
+
+ abstract Class<L> getListType();
+
+ Request getNoArgumentMethodRequest(String method) {
+ HttpUrl url = getUrlBuilder().addPathSegment(method).build();
+ return getRequestBuilder().get().url(url).build();
+ }
+
+ RequestBody getJsonRequestBody(Object object) {
+ return RequestBody.create(JSON, mapToJson(object));
+ }
+
+ void addQueryParameters(Builder urlBuilder, Object object) {
+ Map<String, Object> queryMap = MAPPER.convertValue(object, new TypeReference<Map<String, Object>>() {});
+ queryMap.keySet().forEach(key -> {
+ Object type = queryMap.get(key);
+ if (!(type instanceof String)) {
+ type = mapToJson(type);
+ }
+ urlBuilder.addQueryParameter(key, (String) type);
+ });
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.api.model.CollectionList;
+import org.arvados.client.config.ConfigProvider;
+import org.slf4j.Logger;
+
+public class CollectionsApiClient extends BaseStandardApiClient<Collection, CollectionList> {
+
+ private static final String RESOURCE = "collections";
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(CollectionsApiClient.class);
+
+ public CollectionsApiClient(ConfigProvider config) {
+ super(config);
+ }
+
+ @Override
+ public Collection create(Collection type) {
+ Collection newCollection = super.create(type);
+ log.debug(String.format("New collection '%s' with UUID %s has been created", newCollection.getName(), newCollection.getUuid()));
+ return newCollection;
+ }
+
+ @Override
+ String getResource() {
+ return RESOURCE;
+ }
+
+ @Override
+ Class<Collection> getType() {
+ return Collection.class;
+ }
+
+ @Override
+ Class<CollectionList> getListType() {
+ return CollectionList.class;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.MediaType;
+import okhttp3.RequestBody;
+import okio.BufferedSink;
+import okio.Okio;
+import okio.Source;
+import org.slf4j.Logger;
+
+import java.io.File;
+
+/**
+ * Based on:
+ * {@link} https://gist.github.com/eduardb/dd2dc530afd37108e1ac
+ */
+public class CountingFileRequestBody extends RequestBody {
+
+ private static final int SEGMENT_SIZE = 2048; // okio.Segment.SIZE
+ private static final MediaType CONTENT_BINARY = MediaType.parse(com.google.common.net.MediaType.OCTET_STREAM.toString());
+
+ private final File file;
+ private final ProgressListener listener;
+
+ CountingFileRequestBody(final File file, final ProgressListener listener) {
+ this.file = file;
+ this.listener = listener;
+ }
+
+ @Override
+ public long contentLength() {
+ return file.length();
+ }
+
+ @Override
+ public MediaType contentType() {
+ return CONTENT_BINARY;
+ }
+
+ @Override
+ public void writeTo(BufferedSink sink) {
+ try (Source source = Okio.source(file)) {
+ long total = 0;
+ long read;
+
+ while ((read = source.read(sink.buffer(), SEGMENT_SIZE)) != -1) {
+ total += read;
+ sink.flush();
+ listener.updateProgress(total);
+
+ }
+ } catch (RuntimeException rethrown) {
+ throw rethrown;
+ } catch (Exception ignored) {
+ //ignore
+ }
+ }
+
+ static class TransferData {
+
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(TransferData.class);
+ private int progressValue;
+ private long totalSize;
+
+ TransferData(long totalSize) {
+ this.progressValue = 0;
+ this.totalSize = totalSize;
+ }
+
+ void updateTransferProgress(long transferred) {
+ float progress = (transferred / (float) totalSize) * 100;
+ if (progressValue != (int) progress) {
+ progressValue = (int) progress;
+ log.debug("{} / {} / {}%", transferred, totalSize, progressValue);
+ }
+ }
+ }
+}
\ No newline at end of file
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.HttpUrl;
+import okhttp3.HttpUrl.Builder;
+import okhttp3.Request;
+import okhttp3.RequestBody;
+import org.arvados.client.api.model.Group;
+import org.arvados.client.api.model.GroupList;
+import org.arvados.client.api.model.argument.ContentsGroup;
+import org.arvados.client.api.model.argument.UntrashGroup;
+import org.arvados.client.config.ConfigProvider;
+import org.slf4j.Logger;
+
+public class GroupsApiClient extends BaseStandardApiClient<Group, GroupList> {
+
+ private static final String RESOURCE = "groups";
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(GroupsApiClient.class);
+
+ public GroupsApiClient(ConfigProvider config) {
+ super(config);
+ }
+
+ public GroupList contents(ContentsGroup contentsGroup) {
+ log.debug("Get {} contents", getType().getSimpleName());
+ Builder urlBuilder = getUrlBuilder().addPathSegment("contents");
+ addQueryParameters(urlBuilder, contentsGroup);
+ HttpUrl url = urlBuilder.build();
+ Request request = getRequestBuilder().url(url).build();
+ return callForList(request);
+ }
+
+ public Group untrash(UntrashGroup untrashGroup) {
+ log.debug("Untrash {} by UUID {}", getType().getSimpleName(), untrashGroup.getUuid());
+ HttpUrl url = getUrlBuilder().addPathSegment(untrashGroup.getUuid()).addPathSegment("untrash").build();
+ RequestBody requestBody = getJsonRequestBody(untrashGroup);
+ Request request = getRequestBuilder().post(requestBody).url(url).build();
+ return callForType(request);
+ }
+
+ @Override
+ String getResource() {
+ return RESOURCE;
+ }
+
+ @Override
+ Class<Group> getType() {
+ return Group.class;
+ }
+
+ @Override
+ Class<GroupList> getListType() {
+ return GroupList.class;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.Request;
+import okhttp3.RequestBody;
+import org.arvados.client.api.client.CountingFileRequestBody.TransferData;
+import org.arvados.client.common.Headers;
+import org.arvados.client.config.ConfigProvider;
+import org.slf4j.Logger;
+
+import java.io.File;
+import java.util.Map;
+
+public class KeepServerApiClient extends BaseApiClient {
+
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(KeepServerApiClient.class);
+
+ public KeepServerApiClient(ConfigProvider config) {
+ super(config);
+ }
+
+ public String upload(String url, Map<String, String> headers, File body) {
+
+ log.debug("Upload file {} to server location {}", body, url);
+
+ final TransferData transferData = new TransferData(body.length());
+
+ RequestBody requestBody = new CountingFileRequestBody(body, transferData::updateTransferProgress);
+
+ Request request = getRequestBuilder()
+ .url(url)
+ .addHeader(Headers.X_KEEP_DESIRED_REPLICAS, headers.get(Headers.X_KEEP_DESIRED_REPLICAS))
+ .put(requestBody)
+ .build();
+
+ return newCall(request);
+ }
+
+ public byte[] download(String url) {
+
+ Request request = getRequestBuilder()
+ .url(url)
+ .get()
+ .build();
+
+ return newFileCall(request);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import org.arvados.client.api.model.KeepService;
+import org.arvados.client.api.model.KeepServiceList;
+import org.arvados.client.config.ConfigProvider;
+import org.slf4j.Logger;
+
+public class KeepServicesApiClient extends BaseStandardApiClient<KeepService, KeepServiceList> {
+
+ private static final String RESOURCE = "keep_services";
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(KeepServicesApiClient.class);
+
+ public KeepServicesApiClient(ConfigProvider config) {
+ super(config);
+ }
+
+ public KeepServiceList accessible() {
+ log.debug("Get list of accessible {}", getType().getSimpleName());
+ return callForList(getNoArgumentMethodRequest("accessible"));
+ }
+
+ @Override
+ String getResource() {
+ return RESOURCE;
+ }
+
+ @Override
+ Class<KeepService> getType() {
+ return KeepService.class;
+ }
+
+ @Override
+ Class<KeepServiceList> getListType() {
+ return KeepServiceList.class;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.HttpUrl;
+import okhttp3.Request;
+import org.arvados.client.config.ConfigProvider;
+
+public class KeepWebApiClient extends BaseApiClient {
+
+ public KeepWebApiClient(ConfigProvider config) {
+ super(config);
+ }
+
+ public byte[] download(String collectionUuid, String filePathName) {
+ Request request = getRequestBuilder()
+ .url(getUrlBuilder(collectionUuid,filePathName).build())
+ .get()
+ .build();
+
+ return newFileCall(request);
+ }
+
+ private HttpUrl.Builder getUrlBuilder(String collectionUuid, String filePathName) {
+ return new HttpUrl.Builder()
+ .scheme(config.getApiProtocol())
+ .host(config.getKeepWebHost())
+ .port(config.getKeepWebPort())
+ .addPathSegment("c=" + collectionUuid)
+ .addPathSegment(filePathName);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+@FunctionalInterface
+public interface ProgressListener {
+
+ void updateProgress(long num);
+}
\ No newline at end of file
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.Request;
+import org.arvados.client.api.model.User;
+import org.arvados.client.api.model.UserList;
+import org.arvados.client.config.ConfigProvider;
+import org.slf4j.Logger;
+
+public class UsersApiClient extends BaseStandardApiClient<User, UserList> {
+
+ private static final String RESOURCE = "users";
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(UsersApiClient.class);
+
+ public UsersApiClient(ConfigProvider config) {
+ super(config);
+ }
+
+ public User current() {
+ log.debug("Get current {}", getType().getSimpleName());
+ Request request = getNoArgumentMethodRequest("current");
+ return callForType(request);
+ }
+
+ public User system() {
+ log.debug("Get system {}", getType().getSimpleName());
+ Request request = getNoArgumentMethodRequest("system");
+ return callForType(request);
+ }
+
+ @Override
+ String getResource() {
+ return RESOURCE;
+ }
+
+ @Override
+ Class<User> getType() {
+ return User.class;
+ }
+
+ @Override
+ Class<UserList> getListType() {
+ return UserList.class;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client.factory;
+
+import okhttp3.OkHttpClient;
+import org.arvados.client.exception.ArvadosClientException;
+import org.slf4j.Logger;
+
+import javax.net.ssl.SSLContext;
+import javax.net.ssl.SSLSocketFactory;
+import javax.net.ssl.TrustManager;
+import javax.net.ssl.X509TrustManager;
+import java.security.KeyManagementException;
+import java.security.NoSuchAlgorithmException;
+import java.security.SecureRandom;
+import java.security.cert.X509Certificate;
+
+public class OkHttpClientFactory {
+
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(OkHttpClientFactory.class);
+
+ OkHttpClientFactory() {
+ }
+
+ public static OkHttpClientFactoryBuilder builder() {
+ return new OkHttpClientFactoryBuilder();
+ }
+
+ public OkHttpClient create(boolean apiHostInsecure) {
+ OkHttpClient.Builder builder = new OkHttpClient.Builder();
+ if (apiHostInsecure) {
+ trustAllCertificates(builder);
+ }
+ return builder.build();
+ }
+
+ private void trustAllCertificates(OkHttpClient.Builder builder) {
+ log.warn("Creating unsafe OkHttpClient. All SSL certificates will be accepted.");
+ try {
+ // Create a trust manager that does not validate certificate chains
+ final TrustManager[] trustAllCerts = new TrustManager[] { createX509TrustManager() };
+
+ // Install the all-trusting trust manager
+ SSLContext sslContext = SSLContext.getInstance("SSL");
+ sslContext.init(null, trustAllCerts, new SecureRandom());
+ // Create an ssl socket factory with our all-trusting manager
+ final SSLSocketFactory sslSocketFactory = sslContext.getSocketFactory();
+
+ builder.sslSocketFactory(sslSocketFactory, (X509TrustManager) trustAllCerts[0]);
+ builder.hostnameVerifier((hostname, session) -> true);
+ } catch (NoSuchAlgorithmException | KeyManagementException e) {
+ throw new ArvadosClientException("Error establishing SSL context", e);
+ }
+ }
+
+ private static X509TrustManager createX509TrustManager() {
+ return new X509TrustManager() {
+
+ @Override
+ public void checkClientTrusted(X509Certificate[] chain, String authType) {}
+
+ @Override
+ public void checkServerTrusted(X509Certificate[] chain, String authType) {}
+
+ @Override
+ public X509Certificate[] getAcceptedIssuers() {
+ return new X509Certificate[] {};
+ }
+ };
+ }
+
+ public static class OkHttpClientFactoryBuilder {
+ OkHttpClientFactoryBuilder() {
+ }
+
+ public OkHttpClientFactory build() {
+ return new OkHttpClientFactory();
+ }
+
+ public String toString() {
+ return "OkHttpClientFactory.OkHttpClientFactoryBuilder()";
+ }
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "errors", "error_token" })
+public class ApiError {
+
+ @JsonProperty("errors")
+ private List<String> errors;
+ @JsonProperty("error_token")
+ private String errorToken;
+
+ public List<String> getErrors() {
+ return this.errors;
+ }
+
+ public String getErrorToken() {
+ return this.errorToken;
+ }
+
+ public void setErrors(List<String> errors) {
+ this.errors = errors;
+ }
+
+ public void setErrorToken(String errorToken) {
+ this.errorToken = errorToken;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.time.LocalDateTime;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "portable_data_hash", "replication_desired", "replication_confirmed_at", "replication_confirmed", "manifest_text",
+ "name", "description", "properties", "delete_at", "trash_at", "is_trashed" })
+public class Collection extends Item {
+
+ @JsonProperty("portable_data_hash")
+ private String portableDataHash;
+ @JsonProperty("replication_desired")
+ private Integer replicationDesired;
+ @JsonProperty("replication_confirmed_at")
+ private LocalDateTime replicationConfirmedAt;
+ @JsonProperty("replication_confirmed")
+ private Integer replicationConfirmed;
+ @JsonProperty("manifest_text")
+ private String manifestText;
+ @JsonProperty("name")
+ private String name;
+ @JsonProperty("description")
+ private String description;
+ @JsonProperty("properties")
+ private Object properties;
+ @JsonProperty("delete_at")
+ private LocalDateTime deleteAt;
+ @JsonProperty("trash_at")
+ private LocalDateTime trashAt;
+ @JsonProperty("is_trashed")
+ private Boolean trashed;
+
+ public String getPortableDataHash() {
+ return this.portableDataHash;
+ }
+
+ public Integer getReplicationDesired() {
+ return this.replicationDesired;
+ }
+
+ public LocalDateTime getReplicationConfirmedAt() {
+ return this.replicationConfirmedAt;
+ }
+
+ public Integer getReplicationConfirmed() {
+ return this.replicationConfirmed;
+ }
+
+ public String getManifestText() {
+ return this.manifestText;
+ }
+
+ public String getName() {
+ return this.name;
+ }
+
+ public String getDescription() {
+ return this.description;
+ }
+
+ public Object getProperties() {
+ return this.properties;
+ }
+
+ public LocalDateTime getDeleteAt() {
+ return this.deleteAt;
+ }
+
+ public LocalDateTime getTrashAt() {
+ return this.trashAt;
+ }
+
+ public Boolean getTrashed() {
+ return this.trashed;
+ }
+
+ public void setPortableDataHash(String portableDataHash) {
+ this.portableDataHash = portableDataHash;
+ }
+
+ public void setReplicationDesired(Integer replicationDesired) {
+ this.replicationDesired = replicationDesired;
+ }
+
+ public void setReplicationConfirmedAt(LocalDateTime replicationConfirmedAt) {
+ this.replicationConfirmedAt = replicationConfirmedAt;
+ }
+
+ public void setReplicationConfirmed(Integer replicationConfirmed) {
+ this.replicationConfirmed = replicationConfirmed;
+ }
+
+ public void setManifestText(String manifestText) {
+ this.manifestText = manifestText;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ public void setProperties(Object properties) {
+ this.properties = properties;
+ }
+
+ public void setDeleteAt(LocalDateTime deleteAt) {
+ this.deleteAt = deleteAt;
+ }
+
+ public void setTrashAt(LocalDateTime trashAt) {
+ this.trashAt = trashAt;
+ }
+
+ public void setTrashed(Boolean trashed) {
+ this.trashed = trashed;
+ }
+
+ public String toString() {
+ return "Collection(portableDataHash=" + this.getPortableDataHash() + ", replicationDesired=" + this.getReplicationDesired() + ", replicationConfirmedAt=" + this.getReplicationConfirmedAt() + ", replicationConfirmed=" + this.getReplicationConfirmed() + ", manifestText=" + this.getManifestText() + ", name=" + this.getName() + ", description=" + this.getDescription() + ", properties=" + this.getProperties() + ", deleteAt=" + this.getDeleteAt() + ", trashAt=" + this.getTrashAt() + ", trashed=" + this.getTrashed() + ")";
+ }
+}
\ No newline at end of file
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "items" })
+public class CollectionList extends ItemList {
+
+ @JsonProperty("items")
+ private List<Collection> items;
+
+ public List<Collection> getItems() {
+ return this.items;
+ }
+
+ public void setItems(List<Collection> items) {
+ this.items = items;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.time.LocalDateTime;
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "command", "container_count", "container_count_max", "container_image", "container_uuid", "cwd", "environment", "expires_at",
+ "filters", "log_uuid", "mounts", "output_name", "output_path", "output_uuid", "output_ttl", "priority", "properties", "requesting_container_uuid",
+ "runtime_constraints", "scheduling_parameters", "state", "use_existing" })
+public class Group extends Item {
+
+ @JsonProperty("name")
+ private String name;
+ @JsonProperty("group_class")
+ private String groupClass;
+ @JsonProperty("description")
+ private String description;
+ @JsonProperty("writable_by")
+ private List<String> writableBy;
+ @JsonProperty("delete_at")
+ private LocalDateTime deleteAt;
+ @JsonProperty("trash_at")
+ private LocalDateTime trashAt;
+ @JsonProperty("is_trashed")
+ private Boolean isTrashed;
+ @JsonProperty("command")
+ private List<String> command;
+ @JsonProperty("container_count")
+ private Integer containerCount;
+ @JsonProperty("container_count_max")
+ private Integer containerCountMax;
+ @JsonProperty("container_image")
+ private String containerImage;
+ @JsonProperty("container_uuid")
+ private String containerUuid;
+ @JsonProperty("cwd")
+ private String cwd;
+ @JsonProperty("environment")
+ private Object environment;
+ @JsonProperty("expires_at")
+ private LocalDateTime expiresAt;
+ @JsonProperty("filters")
+ private List<String> filters;
+ @JsonProperty("log_uuid")
+ private String logUuid;
+ @JsonProperty("mounts")
+ private Object mounts;
+ @JsonProperty("output_name")
+ private String outputName;
+ @JsonProperty("output_path")
+ private String outputPath;
+ @JsonProperty("output_uuid")
+ private String outputUuid;
+ @JsonProperty("output_ttl")
+ private Integer outputTtl;
+ @JsonProperty("priority")
+ private Integer priority;
+ @JsonProperty("properties")
+ private Object properties;
+ @JsonProperty("requesting_container_uuid")
+ private String requestingContainerUuid;
+ @JsonProperty("runtime_constraints")
+ private RuntimeConstraints runtimeConstraints;
+ @JsonProperty("scheduling_parameters")
+ private Object schedulingParameters;
+ @JsonProperty("state")
+ private String state;
+ @JsonProperty("use_existing")
+ private Boolean useExisting;
+
+ public String getName() {
+ return this.name;
+ }
+
+ public String getGroupClass() {
+ return this.groupClass;
+ }
+
+ public String getDescription() {
+ return this.description;
+ }
+
+ public List<String> getWritableBy() {
+ return this.writableBy;
+ }
+
+ public LocalDateTime getDeleteAt() {
+ return this.deleteAt;
+ }
+
+ public LocalDateTime getTrashAt() {
+ return this.trashAt;
+ }
+
+ public Boolean getIsTrashed() {
+ return this.isTrashed;
+ }
+
+ public List<String> getCommand() {
+ return this.command;
+ }
+
+ public Integer getContainerCount() {
+ return this.containerCount;
+ }
+
+ public Integer getContainerCountMax() {
+ return this.containerCountMax;
+ }
+
+ public String getContainerImage() {
+ return this.containerImage;
+ }
+
+ public String getContainerUuid() {
+ return this.containerUuid;
+ }
+
+ public String getCwd() {
+ return this.cwd;
+ }
+
+ public Object getEnvironment() {
+ return this.environment;
+ }
+
+ public LocalDateTime getExpiresAt() {
+ return this.expiresAt;
+ }
+
+ public List<String> getFilters() {
+ return this.filters;
+ }
+
+ public String getLogUuid() {
+ return this.logUuid;
+ }
+
+ public Object getMounts() {
+ return this.mounts;
+ }
+
+ public String getOutputName() {
+ return this.outputName;
+ }
+
+ public String getOutputPath() {
+ return this.outputPath;
+ }
+
+ public String getOutputUuid() {
+ return this.outputUuid;
+ }
+
+ public Integer getOutputTtl() {
+ return this.outputTtl;
+ }
+
+ public Integer getPriority() {
+ return this.priority;
+ }
+
+ public Object getProperties() {
+ return this.properties;
+ }
+
+ public String getRequestingContainerUuid() {
+ return this.requestingContainerUuid;
+ }
+
+ public RuntimeConstraints getRuntimeConstraints() {
+ return this.runtimeConstraints;
+ }
+
+ public Object getSchedulingParameters() {
+ return this.schedulingParameters;
+ }
+
+ public String getState() {
+ return this.state;
+ }
+
+ public Boolean getUseExisting() {
+ return this.useExisting;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public void setGroupClass(String groupClass) {
+ this.groupClass = groupClass;
+ }
+
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ public void setWritableBy(List<String> writableBy) {
+ this.writableBy = writableBy;
+ }
+
+ public void setDeleteAt(LocalDateTime deleteAt) {
+ this.deleteAt = deleteAt;
+ }
+
+ public void setTrashAt(LocalDateTime trashAt) {
+ this.trashAt = trashAt;
+ }
+
+ public void setIsTrashed(Boolean isTrashed) {
+ this.isTrashed = isTrashed;
+ }
+
+ public void setCommand(List<String> command) {
+ this.command = command;
+ }
+
+ public void setContainerCount(Integer containerCount) {
+ this.containerCount = containerCount;
+ }
+
+ public void setContainerCountMax(Integer containerCountMax) {
+ this.containerCountMax = containerCountMax;
+ }
+
+ public void setContainerImage(String containerImage) {
+ this.containerImage = containerImage;
+ }
+
+ public void setContainerUuid(String containerUuid) {
+ this.containerUuid = containerUuid;
+ }
+
+ public void setCwd(String cwd) {
+ this.cwd = cwd;
+ }
+
+ public void setEnvironment(Object environment) {
+ this.environment = environment;
+ }
+
+ public void setExpiresAt(LocalDateTime expiresAt) {
+ this.expiresAt = expiresAt;
+ }
+
+ public void setFilters(List<String> filters) {
+ this.filters = filters;
+ }
+
+ public void setLogUuid(String logUuid) {
+ this.logUuid = logUuid;
+ }
+
+ public void setMounts(Object mounts) {
+ this.mounts = mounts;
+ }
+
+ public void setOutputName(String outputName) {
+ this.outputName = outputName;
+ }
+
+ public void setOutputPath(String outputPath) {
+ this.outputPath = outputPath;
+ }
+
+ public void setOutputUuid(String outputUuid) {
+ this.outputUuid = outputUuid;
+ }
+
+ public void setOutputTtl(Integer outputTtl) {
+ this.outputTtl = outputTtl;
+ }
+
+ public void setPriority(Integer priority) {
+ this.priority = priority;
+ }
+
+ public void setProperties(Object properties) {
+ this.properties = properties;
+ }
+
+ public void setRequestingContainerUuid(String requestingContainerUuid) {
+ this.requestingContainerUuid = requestingContainerUuid;
+ }
+
+ public void setRuntimeConstraints(RuntimeConstraints runtimeConstraints) {
+ this.runtimeConstraints = runtimeConstraints;
+ }
+
+ public void setSchedulingParameters(Object schedulingParameters) {
+ this.schedulingParameters = schedulingParameters;
+ }
+
+ public void setState(String state) {
+ this.state = state;
+ }
+
+ public void setUseExisting(Boolean useExisting) {
+ this.useExisting = useExisting;
+ }
+
+ public String toString() {
+ return "Group(name=" + this.getName() + ", groupClass=" + this.getGroupClass() + ", description=" + this.getDescription() + ", writableBy=" + this.getWritableBy() + ", deleteAt=" + this.getDeleteAt() + ", trashAt=" + this.getTrashAt() + ", isTrashed=" + this.getIsTrashed() + ", command=" + this.getCommand() + ", containerCount=" + this.getContainerCount() + ", containerCountMax=" + this.getContainerCountMax() + ", containerImage=" + this.getContainerImage() + ", containerUuid=" + this.getContainerUuid() + ", cwd=" + this.getCwd() + ", environment=" + this.getEnvironment() + ", expiresAt=" + this.getExpiresAt() + ", filters=" + this.getFilters() + ", logUuid=" + this.getLogUuid() + ", mounts=" + this.getMounts() + ", outputName=" + this.getOutputName() + ", outputPath=" + this.getOutputPath() + ", outputUuid=" + this.getOutputUuid() + ", outputTtl=" + this.getOutputTtl() + ", priority=" + this.getPriority() + ", properties=" + this.getProperties() + ", requestingContainerUuid=" + this.getRequestingContainerUuid() + ", runtimeConstraints=" + this.getRuntimeConstraints() + ", schedulingParameters=" + this.getSchedulingParameters() + ", state=" + this.getState() + ", useExisting=" + this.getUseExisting() + ")";
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "items" })
+public class GroupList extends ItemList {
+
+ @JsonProperty("items")
+ private List<Group> items;
+
+ public List<Group> getItems() {
+ return this.items;
+ }
+
+ public void setItems(List<Group> items) {
+ this.items = items;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.time.LocalDateTime;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "href", "kind", "etag", "uuid", "owner_uuid", "created_at", "modified_by_client_uuid",
+ "modified_by_user_uuid", "modified_at", "updated_at" })
+public abstract class Item {
+
+ @JsonProperty("href")
+ private String href;
+ @JsonProperty("kind")
+ private String kind;
+ @JsonProperty("etag")
+ private String etag;
+ @JsonProperty("uuid")
+ private String uuid;
+ @JsonProperty("owner_uuid")
+ private String ownerUuid;
+ @JsonProperty("created_at")
+ private LocalDateTime createdAt;
+ @JsonProperty("modified_by_client_uuid")
+ private String modifiedByClientUuid;
+ @JsonProperty("modified_by_user_uuid")
+ private String modifiedByUserUuid;
+ @JsonProperty("modified_at")
+ private LocalDateTime modifiedAt;
+ @JsonProperty("updated_at")
+ private LocalDateTime updatedAt;
+
+ public String getHref() {
+ return this.href;
+ }
+
+ public String getKind() {
+ return this.kind;
+ }
+
+ public String getEtag() {
+ return this.etag;
+ }
+
+ public String getUuid() {
+ return this.uuid;
+ }
+
+ public String getOwnerUuid() {
+ return this.ownerUuid;
+ }
+
+ public LocalDateTime getCreatedAt() {
+ return this.createdAt;
+ }
+
+ public String getModifiedByClientUuid() {
+ return this.modifiedByClientUuid;
+ }
+
+ public String getModifiedByUserUuid() {
+ return this.modifiedByUserUuid;
+ }
+
+ public LocalDateTime getModifiedAt() {
+ return this.modifiedAt;
+ }
+
+ public LocalDateTime getUpdatedAt() {
+ return this.updatedAt;
+ }
+
+ public void setHref(String href) {
+ this.href = href;
+ }
+
+ public void setKind(String kind) {
+ this.kind = kind;
+ }
+
+ public void setEtag(String etag) {
+ this.etag = etag;
+ }
+
+ public void setUuid(String uuid) {
+ this.uuid = uuid;
+ }
+
+ public void setOwnerUuid(String ownerUuid) {
+ this.ownerUuid = ownerUuid;
+ }
+
+ public void setCreatedAt(LocalDateTime createdAt) {
+ this.createdAt = createdAt;
+ }
+
+ public void setModifiedByClientUuid(String modifiedByClientUuid) {
+ this.modifiedByClientUuid = modifiedByClientUuid;
+ }
+
+ public void setModifiedByUserUuid(String modifiedByUserUuid) {
+ this.modifiedByUserUuid = modifiedByUserUuid;
+ }
+
+ public void setModifiedAt(LocalDateTime modifiedAt) {
+ this.modifiedAt = modifiedAt;
+ }
+
+ public void setUpdatedAt(LocalDateTime updatedAt) {
+ this.updatedAt = updatedAt;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "kind", "etag", "self_link", "offset", "limit", "items_available" })
+public class ItemList {
+
+ @JsonProperty("kind")
+ private String kind;
+ @JsonProperty("etag")
+ private String etag;
+ @JsonProperty("self_link")
+ private String selfLink;
+ @JsonProperty("offset")
+ private Object offset;
+ @JsonProperty("limit")
+ private Object limit;
+ @JsonProperty("items_available")
+ private Integer itemsAvailable;
+
+ public String getKind() {
+ return this.kind;
+ }
+
+ public String getEtag() {
+ return this.etag;
+ }
+
+ public String getSelfLink() {
+ return this.selfLink;
+ }
+
+ public Object getOffset() {
+ return this.offset;
+ }
+
+ public Object getLimit() {
+ return this.limit;
+ }
+
+ public Integer getItemsAvailable() {
+ return this.itemsAvailable;
+ }
+
+ public void setKind(String kind) {
+ this.kind = kind;
+ }
+
+ public void setEtag(String etag) {
+ this.etag = etag;
+ }
+
+ public void setSelfLink(String selfLink) {
+ this.selfLink = selfLink;
+ }
+
+ public void setOffset(Object offset) {
+ this.offset = offset;
+ }
+
+ public void setLimit(Object limit) {
+ this.limit = limit;
+ }
+
+ public void setItemsAvailable(Integer itemsAvailable) {
+ this.itemsAvailable = itemsAvailable;
+ }
+}
\ No newline at end of file
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.*;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "service_host", "service_port", "service_ssl_flag", "service_type", "read_only" })
+public class KeepService extends Item {
+
+ @JsonProperty("service_host")
+ private String serviceHost;
+ @JsonProperty("service_port")
+ private Integer servicePort;
+ @JsonProperty("service_ssl_flag")
+ private Boolean serviceSslFlag;
+ @JsonProperty("service_type")
+ private String serviceType;
+ @JsonProperty("read_only")
+ private Boolean readOnly;
+ @JsonIgnore
+ private String serviceRoot;
+
+ public String getServiceHost() {
+ return this.serviceHost;
+ }
+
+ public Integer getServicePort() {
+ return this.servicePort;
+ }
+
+ public Boolean getServiceSslFlag() {
+ return this.serviceSslFlag;
+ }
+
+ public String getServiceType() {
+ return this.serviceType;
+ }
+
+ public Boolean getReadOnly() {
+ return this.readOnly;
+ }
+
+ public String getServiceRoot() {
+ return this.serviceRoot;
+ }
+
+ public void setServiceHost(String serviceHost) {
+ this.serviceHost = serviceHost;
+ }
+
+ public void setServicePort(Integer servicePort) {
+ this.servicePort = servicePort;
+ }
+
+ public void setServiceSslFlag(Boolean serviceSslFlag) {
+ this.serviceSslFlag = serviceSslFlag;
+ }
+
+ public void setServiceType(String serviceType) {
+ this.serviceType = serviceType;
+ }
+
+ public void setReadOnly(Boolean readOnly) {
+ this.readOnly = readOnly;
+ }
+
+ public void setServiceRoot(String serviceRoot) {
+ this.serviceRoot = serviceRoot;
+ }
+}
\ No newline at end of file
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "items" })
+public class KeepServiceList extends ItemList {
+
+ @JsonProperty("items")
+ private List<KeepService> items;
+
+ public List<KeepService> getItems() {
+ return this.items;
+ }
+
+ public void setItems(List<KeepService> items) {
+ this.items = items;
+ }
+}
\ No newline at end of file
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "API", "vcpus", "ram", "keep_cache_ram" })
+public class RuntimeConstraints {
+
+ @JsonProperty("API")
+ private Boolean api;
+ @JsonProperty("vcpus")
+ private Integer vcpus;
+ @JsonProperty("ram")
+ private Long ram;
+ @JsonProperty("keep_cache_ram")
+ private Long keepCacheRam;
+
+ public Boolean getApi() {
+ return this.api;
+ }
+
+ public Integer getVcpus() {
+ return this.vcpus;
+ }
+
+ public Long getRam() {
+ return this.ram;
+ }
+
+ public Long getKeepCacheRam() {
+ return this.keepCacheRam;
+ }
+
+ public void setApi(Boolean api) {
+ this.api = api;
+ }
+
+ public void setVcpus(Integer vcpus) {
+ this.vcpus = vcpus;
+ }
+
+ public void setRam(Long ram) {
+ this.ram = ram;
+ }
+
+ public void setKeepCacheRam(Long keepCacheRam) {
+ this.keepCacheRam = keepCacheRam;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "email", "username", "full_name", "first_name", "last_name", "identity_url", "is_active", "is_admin", "is_invited",
+ "prefs", "writable_by", "default_owner_uuid" })
+public class User extends Item {
+
+ @JsonProperty("email")
+ private String email;
+ @JsonProperty("username")
+ private String username;
+ @JsonProperty("full_name")
+ private String fullName;
+ @JsonProperty("first_name")
+ private String firstName;
+ @JsonProperty("last_name")
+ private String lastName;
+ @JsonProperty("identity_url")
+ private String identityUrl;
+ @JsonProperty("is_active")
+ private Boolean isActive;
+ @JsonProperty("is_admin")
+ private Boolean isAdmin;
+ @JsonProperty("is_invited")
+ private Boolean isInvited;
+ @JsonProperty("prefs")
+ private Object prefs;
+ @JsonProperty("writable_by")
+ private List<String> writableBy;
+ @JsonProperty("default_owner_uuid")
+ private Boolean defaultOwnerUuid;
+
+ public String getEmail() {
+ return this.email;
+ }
+
+ public String getUsername() {
+ return this.username;
+ }
+
+ public String getFullName() {
+ return this.fullName;
+ }
+
+ public String getFirstName() {
+ return this.firstName;
+ }
+
+ public String getLastName() {
+ return this.lastName;
+ }
+
+ public String getIdentityUrl() {
+ return this.identityUrl;
+ }
+
+ public Boolean getIsActive() {
+ return this.isActive;
+ }
+
+ public Boolean getIsAdmin() {
+ return this.isAdmin;
+ }
+
+ public Boolean getIsInvited() {
+ return this.isInvited;
+ }
+
+ public Object getPrefs() {
+ return this.prefs;
+ }
+
+ public List<String> getWritableBy() {
+ return this.writableBy;
+ }
+
+ public Boolean getDefaultOwnerUuid() {
+ return this.defaultOwnerUuid;
+ }
+
+ public void setEmail(String email) {
+ this.email = email;
+ }
+
+ public void setUsername(String username) {
+ this.username = username;
+ }
+
+ public void setFullName(String fullName) {
+ this.fullName = fullName;
+ }
+
+ public void setFirstName(String firstName) {
+ this.firstName = firstName;
+ }
+
+ public void setLastName(String lastName) {
+ this.lastName = lastName;
+ }
+
+ public void setIdentityUrl(String identityUrl) {
+ this.identityUrl = identityUrl;
+ }
+
+ public void setIsActive(Boolean isActive) {
+ this.isActive = isActive;
+ }
+
+ public void setIsAdmin(Boolean isAdmin) {
+ this.isAdmin = isAdmin;
+ }
+
+ public void setIsInvited(Boolean isInvited) {
+ this.isInvited = isInvited;
+ }
+
+ public void setPrefs(Object prefs) {
+ this.prefs = prefs;
+ }
+
+ public void setWritableBy(List<String> writableBy) {
+ this.writableBy = writableBy;
+ }
+
+ public void setDefaultOwnerUuid(Boolean defaultOwnerUuid) {
+ this.defaultOwnerUuid = defaultOwnerUuid;
+ }
+
+ public String toString() {
+ return "User(email=" + this.getEmail() + ", username=" + this.getUsername() + ", fullName=" + this.getFullName() + ", firstName=" + this.getFirstName() + ", lastName=" + this.getLastName() + ", identityUrl=" + this.getIdentityUrl() + ", isActive=" + this.getIsActive() + ", isAdmin=" + this.getIsAdmin() + ", isInvited=" + this.getIsInvited() + ", prefs=" + this.getPrefs() + ", writableBy=" + this.getWritableBy() + ", defaultOwnerUuid=" + this.getDefaultOwnerUuid() + ")";
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "items" })
+public class UserList extends ItemList {
+
+ @JsonProperty("items")
+ private List<User> items;
+
+ public List<User> getItems() {
+ return this.items;
+ }
+
+ public void setItems(List<User> items) {
+ this.items = items;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model.argument;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
+public abstract class Argument {
+
+ @JsonIgnore
+ private String uuid;
+
+ public String getUuid() {
+ return this.uuid;
+ }
+
+ public void setUuid(String uuid) {
+ this.uuid = uuid;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model.argument;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonPropertyOrder({ "limit", "order", "filters", "recursive" })
+public class ContentsGroup extends Argument {
+
+ @JsonProperty("limit")
+ private Integer limit;
+
+ @JsonProperty("order")
+ private String order;
+
+ @JsonProperty("filters")
+ private List<String> filters;
+
+ @JsonProperty("recursive")
+ private Boolean recursive;
+
+ public Integer getLimit() {
+ return this.limit;
+ }
+
+ public String getOrder() {
+ return this.order;
+ }
+
+ public List<String> getFilters() {
+ return this.filters;
+ }
+
+ public Boolean getRecursive() {
+ return this.recursive;
+ }
+
+ public void setLimit(Integer limit) {
+ this.limit = limit;
+ }
+
+ public void setOrder(String order) {
+ this.order = order;
+ }
+
+ public void setFilters(List<String> filters) {
+ this.filters = filters;
+ }
+
+ public void setRecursive(Boolean recursive) {
+ this.recursive = recursive;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model.argument;
+
+import com.fasterxml.jackson.annotation.JsonFormat;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+@JsonFormat(shape = JsonFormat.Shape.ARRAY)
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonPropertyOrder({ "attribute", "operator", "operand" })
+public class Filter {
+
+ @JsonProperty("attribute")
+ private String attribute;
+
+ @JsonProperty("operator")
+ private Operator operator;
+
+ @JsonProperty("operand")
+ private Object operand;
+
+ private Filter(String attribute, Operator operator, Object operand) {
+ this.attribute = attribute;
+ this.operator = operator;
+ this.operand = operand;
+ }
+
+ public static Filter of(String attribute, Operator operator, Object operand) {
+ return new Filter(attribute, operator, operand);
+ }
+
+ public String getAttribute() {
+ return this.attribute;
+ }
+
+ public Operator getOperator() {
+ return this.operator;
+ }
+
+ public Object getOperand() {
+ return this.operand;
+ }
+
+ public boolean equals(Object o) {
+ if (o == this) return true;
+ if (!(o instanceof Filter)) return false;
+ final Filter other = (Filter) o;
+ final Object this$attribute = this.getAttribute();
+ final Object other$attribute = other.getAttribute();
+ if (this$attribute == null ? other$attribute != null : !this$attribute.equals(other$attribute)) return false;
+ final Object this$operator = this.getOperator();
+ final Object other$operator = other.getOperator();
+ if (this$operator == null ? other$operator != null : !this$operator.equals(other$operator)) return false;
+ final Object this$operand = this.getOperand();
+ final Object other$operand = other.getOperand();
+ if (this$operand == null ? other$operand != null : !this$operand.equals(other$operand)) return false;
+ return true;
+ }
+
+ public int hashCode() {
+ final int PRIME = 59;
+ int result = 1;
+ final Object $attribute = this.getAttribute();
+ result = result * PRIME + ($attribute == null ? 43 : $attribute.hashCode());
+ final Object $operator = this.getOperator();
+ result = result * PRIME + ($operator == null ? 43 : $operator.hashCode());
+ final Object $operand = this.getOperand();
+ result = result * PRIME + ($operand == null ? 43 : $operand.hashCode());
+ return result;
+ }
+
+ public String toString() {
+ return "Filter(attribute=" + this.getAttribute() + ", operator=" + this.getOperator() + ", operand=" + this.getOperand() + ")";
+ }
+
+ public enum Operator {
+
+ @JsonProperty("<")
+ LESS,
+
+ @JsonProperty("<=")
+ LESS_EQUALS,
+
+ @JsonProperty(">=")
+ MORE_EQUALS,
+
+ @JsonProperty(">")
+ MORE,
+
+ @JsonProperty("like")
+ LIKE,
+
+ @JsonProperty("ilike")
+ ILIKE,
+
+ @JsonProperty("=")
+ EQUALS,
+
+ @JsonProperty("!=")
+ NOT_EQUALS,
+
+ @JsonProperty("in")
+ IN,
+
+ @JsonProperty("not in")
+ NOT_IN,
+
+ @JsonProperty("is_a")
+ IS_A
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model.argument;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonPropertyOrder({ "limit", "offset", "filters", "order", "select", "distinct", "count" })
+public class ListArgument extends Argument {
+
+ @JsonProperty("limit")
+ private Integer limit;
+
+ @JsonProperty("offset")
+ private Integer offset;
+
+ @JsonProperty("filters")
+ private List<Filter> filters;
+
+ @JsonProperty("order")
+ private List<String> order;
+
+ @JsonProperty("select")
+ private List<String> select;
+
+ @JsonProperty("distinct")
+ private Boolean distinct;
+
+ @JsonProperty("count")
+ private Count count;
+
+
+ ListArgument(Integer limit, Integer offset, List<Filter> filters, List<String> order, List<String> select, Boolean distinct, Count count) {
+ this.limit = limit;
+ this.offset = offset;
+ this.filters = filters;
+ this.order = order;
+ this.select = select;
+ this.distinct = distinct;
+ this.count = count;
+ }
+
+ public static ListArgumentBuilder builder() {
+ return new ListArgumentBuilder();
+ }
+
+ public enum Count {
+
+ @JsonProperty("exact")
+ EXACT,
+
+ @JsonProperty("none")
+ NONE
+ }
+
+ public static class ListArgumentBuilder {
+ private Integer limit;
+ private Integer offset;
+ private List<Filter> filters;
+ private List<String> order;
+ private List<String> select;
+ private Boolean distinct;
+ private Count count;
+
+ ListArgumentBuilder() {
+ }
+
+ public ListArgumentBuilder limit(Integer limit) {
+ this.limit = limit;
+ return this;
+ }
+
+ public ListArgumentBuilder offset(Integer offset) {
+ this.offset = offset;
+ return this;
+ }
+
+ public ListArgumentBuilder filters(List<Filter> filters) {
+ this.filters = filters;
+ return this;
+ }
+
+ public ListArgumentBuilder order(List<String> order) {
+ this.order = order;
+ return this;
+ }
+
+ public ListArgumentBuilder select(List<String> select) {
+ this.select = select;
+ return this;
+ }
+
+ public ListArgumentBuilder distinct(Boolean distinct) {
+ this.distinct = distinct;
+ return this;
+ }
+
+ public ListArgumentBuilder count(Count count) {
+ this.count = count;
+ return this;
+ }
+
+ public ListArgument build() {
+ return new ListArgument(limit, offset, filters, order, select, distinct, count);
+ }
+
+ public String toString() {
+ return "ListArgument.ListArgumentBuilder(limit=" + this.limit +
+ ", offset=" + this.offset + ", filters=" + this.filters +
+ ", order=" + this.order + ", select=" + this.select +
+ ", distinct=" + this.distinct + ", count=" + this.count + ")";
+ }
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model.argument;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonPropertyOrder({ "ensure_unique_name" })
+public class UntrashGroup extends Argument {
+
+ @JsonProperty("ensure_unique_name")
+ private Boolean ensureUniqueName;
+
+ public Boolean getEnsureUniqueName() {
+ return this.ensureUniqueName;
+ }
+
+ public void setEnsureUniqueName(Boolean ensureUniqueName) {
+ this.ensureUniqueName = ensureUniqueName;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.common;
+
+public final class Characters {
+
+ private Characters() {}
+
+ public static final String SPACE = "\\040";
+ public static final String NEW_LINE = "\n";
+ public static final String SLASH = "/";
+ public static final String DOT = ".";
+ public static final String COLON = ":";
+ public static final String PERCENT = "%";
+ public static final String QUOTE = "\"";
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.common;
+
+public final class Headers {
+
+ private Headers() {}
+
+ public static final String X_KEEP_DESIRED_REPLICAS = "X-Keep-Desired-Replicas";
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.common;
+
+public final class Patterns {
+
+ public static final String HINT_PATTERN = "^[A-Z][A-Za-z0-9@_-]+$";
+ public static final String FILE_TOKEN_PATTERN = "(\\d+:\\d+:\\S+)";
+ public static final String LOCATOR_PATTERN = "([0-9a-f]{32})\\+([0-9]+)(\\+[A-Z][-A-Za-z0-9@_]*)*";
+ public static final String GROUP_UUID_PATTERN = "[a-z0-9]{5}-j7d0g-[a-z0-9]{15}";
+ public static final String USER_UUID_PATTERN = "[a-z0-9]{5}-tpzed-[a-z0-9]{15}";
+
+ private Patterns() {}
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.config;
+
+import java.io.File;
+
+public interface ConfigProvider {
+
+ //API
+ boolean isApiHostInsecure();
+
+ String getKeepWebHost();
+
+ int getKeepWebPort();
+
+ String getApiHost();
+
+ int getApiPort();
+
+ String getApiToken();
+
+ String getApiProtocol();
+
+
+ //FILE UPLOAD
+ int getFileSplitSize();
+
+ File getFileSplitDirectory();
+
+ int getNumberOfCopies();
+
+ int getNumberOfRetries();
+
+
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.config;
+
+import java.io.File;
+
+public class ExternalConfigProvider implements ConfigProvider {
+
+ private boolean apiHostInsecure;
+ private String keepWebHost;
+ private int keepWebPort;
+ private String apiHost;
+ private int apiPort;
+ private String apiToken;
+ private String apiProtocol;
+ private int fileSplitSize;
+ private File fileSplitDirectory;
+ private int numberOfCopies;
+ private int numberOfRetries;
+
+ ExternalConfigProvider(boolean apiHostInsecure, String keepWebHost, int keepWebPort, String apiHost, int apiPort, String apiToken, String apiProtocol, int fileSplitSize, File fileSplitDirectory, int numberOfCopies, int numberOfRetries) {
+ this.apiHostInsecure = apiHostInsecure;
+ this.keepWebHost = keepWebHost;
+ this.keepWebPort = keepWebPort;
+ this.apiHost = apiHost;
+ this.apiPort = apiPort;
+ this.apiToken = apiToken;
+ this.apiProtocol = apiProtocol;
+ this.fileSplitSize = fileSplitSize;
+ this.fileSplitDirectory = fileSplitDirectory;
+ this.numberOfCopies = numberOfCopies;
+ this.numberOfRetries = numberOfRetries;
+ }
+
+ public static ExternalConfigProviderBuilder builder() {
+ return new ExternalConfigProviderBuilder();
+ }
+
+ @Override
+ public String toString() {
+ return "ExternalConfigProvider{" +
+ "apiHostInsecure=" + apiHostInsecure +
+ ", keepWebHost='" + keepWebHost + '\'' +
+ ", keepWebPort=" + keepWebPort +
+ ", apiHost='" + apiHost + '\'' +
+ ", apiPort=" + apiPort +
+ ", apiToken='" + apiToken + '\'' +
+ ", apiProtocol='" + apiProtocol + '\'' +
+ ", fileSplitSize=" + fileSplitSize +
+ ", fileSplitDirectory=" + fileSplitDirectory +
+ ", numberOfCopies=" + numberOfCopies +
+ ", numberOfRetries=" + numberOfRetries +
+ '}';
+ }
+
+ public boolean isApiHostInsecure() {
+ return this.apiHostInsecure;
+ }
+
+ public String getKeepWebHost() {
+ return this.keepWebHost;
+ }
+
+ public int getKeepWebPort() {
+ return this.keepWebPort;
+ }
+
+ public String getApiHost() {
+ return this.apiHost;
+ }
+
+ public int getApiPort() {
+ return this.apiPort;
+ }
+
+ public String getApiToken() {
+ return this.apiToken;
+ }
+
+ public String getApiProtocol() {
+ return this.apiProtocol;
+ }
+
+ public int getFileSplitSize() {
+ return this.fileSplitSize;
+ }
+
+ public File getFileSplitDirectory() {
+ return this.fileSplitDirectory;
+ }
+
+ public int getNumberOfCopies() {
+ return this.numberOfCopies;
+ }
+
+ public int getNumberOfRetries() {
+ return this.numberOfRetries;
+ }
+
+ public static class ExternalConfigProviderBuilder {
+ private boolean apiHostInsecure;
+ private String keepWebHost;
+ private int keepWebPort;
+ private String apiHost;
+ private int apiPort;
+ private String apiToken;
+ private String apiProtocol;
+ private int fileSplitSize;
+ private File fileSplitDirectory;
+ private int numberOfCopies;
+ private int numberOfRetries;
+
+ ExternalConfigProviderBuilder() {
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder apiHostInsecure(boolean apiHostInsecure) {
+ this.apiHostInsecure = apiHostInsecure;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder keepWebHost(String keepWebHost) {
+ this.keepWebHost = keepWebHost;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder keepWebPort(int keepWebPort) {
+ this.keepWebPort = keepWebPort;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder apiHost(String apiHost) {
+ this.apiHost = apiHost;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder apiPort(int apiPort) {
+ this.apiPort = apiPort;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder apiToken(String apiToken) {
+ this.apiToken = apiToken;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder apiProtocol(String apiProtocol) {
+ this.apiProtocol = apiProtocol;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder fileSplitSize(int fileSplitSize) {
+ this.fileSplitSize = fileSplitSize;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder fileSplitDirectory(File fileSplitDirectory) {
+ this.fileSplitDirectory = fileSplitDirectory;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder numberOfCopies(int numberOfCopies) {
+ this.numberOfCopies = numberOfCopies;
+ return this;
+ }
+
+ public ExternalConfigProvider.ExternalConfigProviderBuilder numberOfRetries(int numberOfRetries) {
+ this.numberOfRetries = numberOfRetries;
+ return this;
+ }
+
+ public ExternalConfigProvider build() {
+ return new ExternalConfigProvider(apiHostInsecure, keepWebHost, keepWebPort, apiHost, apiPort, apiToken, apiProtocol, fileSplitSize, fileSplitDirectory, numberOfCopies, numberOfRetries);
+ }
+
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.config;
+
+import com.typesafe.config.Config;
+import com.typesafe.config.ConfigFactory;
+
+import java.io.File;
+
+public class FileConfigProvider implements ConfigProvider {
+
+ private static final String DEFAULT_PATH = "arvados";
+ private final Config config;
+
+ public FileConfigProvider() {
+ config = ConfigFactory.load().getConfig(DEFAULT_PATH);
+ }
+
+ public FileConfigProvider(final String configFile) {
+ config = (configFile != null) ?
+ ConfigFactory.load(configFile).getConfig(DEFAULT_PATH) : ConfigFactory.load().getConfig(DEFAULT_PATH);
+ }
+
+ public Config getConfig() {
+ return config;
+ }
+
+ private File getFile(String path) {
+ return new File(config.getString(path));
+ }
+
+ private int getInt(String path) {
+ return config.getInt(path);
+ }
+
+ private boolean getBoolean(String path) {
+ return config.getBoolean(path);
+ }
+
+ private String getString(String path) {
+ return config.getString(path);
+ }
+
+ @Override
+ public boolean isApiHostInsecure() {
+ return this.getBoolean("api.host-insecure");
+ }
+
+ @Override
+ public String getKeepWebHost() {
+ return this.getString("api.keepweb-host");
+ }
+
+ @Override
+ public int getKeepWebPort() {
+ return this.getInt("api.keepweb-port");
+ }
+
+ @Override
+ public String getApiHost() {
+ return this.getString("api.host");
+ }
+
+ @Override
+ public int getApiPort() {
+ return this.getInt("api.port");
+ }
+
+ @Override
+ public String getApiToken() {
+ return this.getString("api.token");
+ }
+
+ @Override
+ public String getApiProtocol() {
+ return this.getString("api.protocol");
+ }
+
+ @Override
+ public int getFileSplitSize() {
+ return this.getInt("split-size");
+ }
+
+ @Override
+ public File getFileSplitDirectory() {
+ return this.getFile("temp-dir");
+ }
+
+ @Override
+ public int getNumberOfCopies() {
+ return this.getInt("copies");
+ }
+
+ @Override
+ public int getNumberOfRetries() {
+ return this.getInt("retries");
+ }
+
+ public String getIntegrationTestProjectUuid() {
+ return this.getString("integration-tests.project-uuid");
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.exception;
+
+public class ArvadosApiException extends ArvadosClientException {
+
+ private static final long serialVersionUID = 1L;
+
+ public ArvadosApiException(String message) {
+ super(message);
+ }
+
+ public ArvadosApiException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+ public ArvadosApiException(Throwable cause) {
+ super(cause);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.exception;
+
+/**
+ * Parent exception for all exceptions in library.
+ * More specific exceptions like ArvadosApiException extend this class.
+ */
+public class ArvadosClientException extends RuntimeException {
+
+ public ArvadosClientException(String message) {
+ super(message);
+ }
+
+ public ArvadosClientException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+ public ArvadosClientException(Throwable cause) {
+ super(cause);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.facade;
+
+import com.google.common.collect.Lists;
+import org.arvados.client.api.client.CollectionsApiClient;
+import org.arvados.client.api.client.GroupsApiClient;
+import org.arvados.client.api.client.KeepWebApiClient;
+import org.arvados.client.api.client.UsersApiClient;
+import org.arvados.client.api.model.*;
+import org.arvados.client.api.model.argument.Filter;
+import org.arvados.client.api.model.argument.ListArgument;
+import org.arvados.client.config.FileConfigProvider;
+import org.arvados.client.config.ConfigProvider;
+import org.arvados.client.logic.collection.FileToken;
+import org.arvados.client.logic.collection.ManifestDecoder;
+import org.arvados.client.logic.keep.FileDownloader;
+import org.arvados.client.logic.keep.FileUploader;
+import org.arvados.client.logic.keep.KeepClient;
+import org.slf4j.Logger;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+public class ArvadosFacade {
+
+ private final ConfigProvider config;
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(ArvadosFacade.class);
+ private CollectionsApiClient collectionsApiClient;
+ private GroupsApiClient groupsApiClient;
+ private UsersApiClient usersApiClient;
+ private FileDownloader fileDownloader;
+ private FileUploader fileUploader;
+ private static final String PROJECT = "project";
+ private static final String SUBPROJECT = "sub-project";
+
+ public ArvadosFacade(ConfigProvider config) {
+ this.config = config;
+ setFacadeFields();
+ }
+
+ public ArvadosFacade() {
+ this.config = new FileConfigProvider();
+ setFacadeFields();
+ }
+
+ private void setFacadeFields() {
+ collectionsApiClient = new CollectionsApiClient(config);
+ groupsApiClient = new GroupsApiClient(config);
+ usersApiClient = new UsersApiClient(config);
+ KeepClient keepClient = new KeepClient(config);
+ ManifestDecoder manifestDecoder = new ManifestDecoder();
+ KeepWebApiClient keepWebApiClient = new KeepWebApiClient(config);
+ fileDownloader = new FileDownloader(keepClient, manifestDecoder, collectionsApiClient, keepWebApiClient);
+ fileUploader = new FileUploader(keepClient, collectionsApiClient, config);
+ }
+
+ /**
+ * This method downloads single file from collection using Arvados Keep-Web.
+ * File is saved on a drive in specified location and returned.
+ *
+ * @param filePathName path to the file in collection. If requested file is stored
+ * directly in collection (not within its subdirectory) this
+ * would be just the name of file (ex. 'file.txt').
+ * Otherwise full file path must be passed (ex. 'folder/file.txt')
+ * @param collectionUuid uuid of collection containing requested file
+ * @param pathToDownloadFolder path to location in which file should be saved.
+ * Passed location must be a directory in which file of
+ * that name does not already exist.
+ * @return downloaded file
+ */
+ public File downloadFile(String filePathName, String collectionUuid, String pathToDownloadFolder) {
+ return fileDownloader.downloadSingleFileUsingKeepWeb(filePathName, collectionUuid, pathToDownloadFolder);
+ }
+
+ /**
+ * This method downloads all files from collection.
+ * Directory named by collection uuid is created in specified location,
+ * files are saved on a drive in this directory and list with downloaded
+ * files is returned.
+ *
+ * @param collectionUuid uuid of collection from which files are downloaded
+ * @param pathToDownloadFolder path to location in which files should be saved.
+ * New folder named by collection uuid, containing
+ * downloaded files, is created in this location.
+ * Passed location must be a directory in which folder
+ * of that name does not already exist.
+ * @param usingKeepWeb if set to true files will be downloaded using Keep Web.
+ * If set to false files will be downloaded using Keep Server API.
+ * @return list containing downloaded files
+ */
+ public List<File> downloadCollectionFiles(String collectionUuid, String pathToDownloadFolder, boolean usingKeepWeb) {
+ if (usingKeepWeb)
+ return fileDownloader.downloadFilesFromCollectionUsingKeepWeb(collectionUuid, pathToDownloadFolder);
+ return fileDownloader.downloadFilesFromCollection(collectionUuid, pathToDownloadFolder);
+ }
+
+ /**
+ * Lists all FileTokens (objects containing information about files) for
+ * specified collection.
+ * Information in each FileToken includes file path, name, size and position
+ * in data stream
+ *
+ * @param collectionUuid uuid of collection for which FileTokens are listed
+ * @return list containing FileTokens for each file in specified collection
+ */
+ public List<FileToken> listFileInfoFromCollection(String collectionUuid) {
+ return fileDownloader.listFileInfoFromCollection(collectionUuid);
+ }
+
+ /**
+ * Creates and uploads new collection containing passed files.
+ * Created collection has a default name and is uploaded to user's 'Home' project.
+ *
+ * @see ArvadosFacade#upload(List, String, String)
+ * @param files list of files to be uploaded within new collection
+ * @return collection object mapped from JSON that is returned from server after successful upload
+ */
+ public Collection upload(List<File> files) {
+ return upload(files, null, null);
+ }
+
+ /**
+ * Creates and uploads new collection containing a single file.
+ * Created collection has a default name and is uploaded to user's 'Home' project.
+ *
+ * @see ArvadosFacade#upload(List, String, String)
+ * @param file file to be uploaded
+ * @return collection object mapped from JSON that is returned from server after successful upload
+ */
+ public Collection upload(File file) {
+ return upload(Collections.singletonList(file), null, null);
+ }
+
+ /**
+ * Uploads new collection with specified name and containing selected files
+ * to an existing project.
+ *
+ * @param sourceFiles list of files to be uploaded within new collection
+ * @param collectionName name for the newly created collection.
+ * Collection with that name cannot be already created
+ * in specified project. If null is passed
+ * then collection name is set to default, containing
+ * phrase 'New Collection' and a timestamp.
+ * @param projectUuid uuid of the project in which created collection is to be included.
+ * If null is passed then collection is uploaded to user's 'Home' project.
+ * @return collection object mapped from JSON that is returned from server after successful upload
+ */
+ public Collection upload(List<File> sourceFiles, String collectionName, String projectUuid) {
+ return fileUploader.upload(sourceFiles, collectionName, projectUuid);
+ }
+
+ /**
+ * Uploads a file to a specified collection.
+ *
+ * @see ArvadosFacade#uploadToExistingCollection(List, String)
+ * @param file file to be uploaded to existing collection. Filenames must be unique
+ * in comparison with files already existing within collection.
+ * @param collectionUUID UUID of collection to which files should be uploaded
+ * @return collection object mapped from JSON that is returned from server after successful upload
+ */
+ public Collection uploadToExistingCollection(File file, String collectionUUID) {
+ return fileUploader.uploadToExistingCollection(Collections.singletonList(file), collectionUUID);
+ }
+
+ /**
+ * Uploads multiple files to an existing collection.
+ *
+ * @param files list of files to be uploaded to existing collection.
+ * File names must be unique - both within passed list and
+ * in comparison with files already existing within collection.
+ * @param collectionUUID UUID of collection to which files should be uploaded
+ * @return collection object mapped from JSON that is returned from server after successful upload
+ */
+ public Collection uploadToExistingCollection(List<File> files, String collectionUUID) {
+ return fileUploader.uploadToExistingCollection(files, collectionUUID);
+ }
+
+ /**
+ * Creates and uploads new empty collection to specified project.
+ *
+ * @param collectionName name for the newly created collection.
+ * Collection with that name cannot be already created
+ * in specified project.
+ * @param projectUuid uuid of project that will contain uploaded empty collection.
+ * To select home project pass current user's uuid from getCurrentUser()
+ * @return collection object mapped from JSON that is returned from server after successful upload
+ * @see ArvadosFacade#getCurrentUser()
+ */
+ public Collection createEmptyCollection(String collectionName, String projectUuid) {
+ Collection collection = new Collection();
+ collection.setOwnerUuid(projectUuid);
+ collection.setName(collectionName);
+ return collectionsApiClient.create(collection);
+ }
+
+ /**
+ * Returns current user information based on Api Token provided via configuration
+ *
+ * @return user object mapped from JSON that is returned from server based on provided Api Token.
+ * It contains information about user who has this token assigned.
+ */
+ public User getCurrentUser() {
+ return usersApiClient.current();
+ }
+
+ /**
+ * Gets uuid of current user based on api Token provided in configuration and uses it to list all
+ * projects that this user owns in Arvados.
+ *
+ * @return GroupList containing all groups that current user is owner of.
+ * @see ArvadosFacade#getCurrentUser()
+ */
+ public GroupList showGroupsOwnedByCurrentUser() {
+ ListArgument listArgument = ListArgument.builder()
+ .filters(Arrays.asList(
+ Filter.of("owner_uuid", Filter.Operator.LIKE, getCurrentUser().getUuid()),
+ Filter.of("group_class", Filter.Operator.IN, Lists.newArrayList(PROJECT, SUBPROJECT)
+ )))
+ .build();
+ GroupList groupList = groupsApiClient.list(listArgument);
+ log.debug("Groups owned by user:");
+ groupList.getItems().forEach(m -> log.debug(m.getUuid() + " -- " + m.getName()));
+
+ return groupList;
+ }
+
+ /**
+ * Gets uuid of current user based on api Token provided in configuration and uses it to list all
+ * projects that this user has read access to in Arvados.
+ *
+ * @return GroupList containing all groups that current user has read access to.
+ */
+ public GroupList showGroupsAccessibleByCurrentUser() {
+ ListArgument listArgument = ListArgument.builder()
+ .filters(Collections.singletonList(
+ Filter.of("group_class", Filter.Operator.IN, Lists.newArrayList(PROJECT, SUBPROJECT)
+ )))
+ .build();
+ GroupList groupList = groupsApiClient.list(listArgument);
+ log.debug("Groups accessible by user:");
+ groupList.getItems().forEach(m -> log.debug(m.getUuid() + " -- " + m.getName()));
+
+ return groupList;
+ }
+
+ /**
+ * Filters all collections from selected project and returns list of those that contain passed String in their name.
+ * Operator "LIKE" is used so in order to obtain certain collection it is sufficient to pass just part of its name.
+ * Returned collections in collectionList are ordered by date of creation (starting from oldest one).
+ *
+ * @param collectionName collections containing this param in their name will be returned.
+ * Passing a wildcard is possible - for example passing "a%" searches for
+ * all collections starting with "a".
+ * @param projectUuid uuid of project in which will be searched for collections with given name. To search home
+ * project provide user uuid (from getCurrentUser())
+ * @return object CollectionList containing all collections matching specified name criteria
+ * @see ArvadosFacade#getCurrentUser()
+ */
+ public CollectionList getCollectionsFromProjectByName(String collectionName, String projectUuid) {
+ ListArgument listArgument = ListArgument.builder()
+ .filters(Arrays.asList(
+ Filter.of("owner_uuid", Filter.Operator.LIKE, projectUuid),
+ Filter.of("name", Filter.Operator.LIKE, collectionName)
+ ))
+ .order(Collections.singletonList("created_at"))
+ .build();
+
+ return collectionsApiClient.list(listArgument);
+ }
+
+ /**
+ * Creates new project that will be a subproject of "home" for current user.
+ *
+ * @param projectName name for the newly created project
+ * @return Group object containing information about created project
+ * (mapped from JSON returned from server after creating the project)
+ */
+ public Group createNewProject(String projectName) {
+ Group project = new Group();
+ project.setName(projectName);
+ project.setGroupClass(PROJECT);
+ Group createdProject = groupsApiClient.create(project);
+ log.debug("Project " + createdProject.getName() + " created with UUID: " + createdProject.getUuid());
+ return createdProject;
+ }
+
+ /**
+ * Deletes collection with specified uuid.
+ *
+ * @param collectionUuid uuid of collection to be deleted. User whose token is provided in configuration
+ * must be authorized to delete such collection.
+ * @return collection object with deleted collection (mapped from JSON returned from server after deleting the collection)
+ */
+ public Collection deleteCollection(String collectionUuid) {
+ Collection deletedCollection = collectionsApiClient.delete(collectionUuid);
+ log.debug("Collection: " + collectionUuid + " deleted.");
+ return deletedCollection;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+import org.arvados.client.api.client.GroupsApiClient;
+import org.arvados.client.api.client.UsersApiClient;
+import org.arvados.client.exception.ArvadosApiException;
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.common.Patterns;
+import org.arvados.client.config.FileConfigProvider;
+import org.arvados.client.config.ConfigProvider;
+import org.arvados.client.exception.ArvadosClientException;
+
+import java.io.File;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
+import java.util.List;
+import java.util.Optional;
+
+public class CollectionFactory {
+
+ private ConfigProvider config;
+ private UsersApiClient usersApiClient;
+ private GroupsApiClient groupsApiClient;
+
+ private final String name;
+ private final String projectUuid;
+ private final List<File> manifestFiles;
+ private final List<String> manifestLocators;
+
+ private CollectionFactory(ConfigProvider config, String name, String projectUuid, List<File> manifestFiles, List<String> manifestLocators) {
+ this.name = name;
+ this.projectUuid = projectUuid;
+ this.manifestFiles = manifestFiles;
+ this.manifestLocators = manifestLocators;
+ this.config = config;
+ setApiClients();
+ }
+
+ public static CollectionFactoryBuilder builder() {
+ return new CollectionFactoryBuilder();
+ }
+
+ private void setApiClients() {
+ if(this.config == null) this.config = new FileConfigProvider();
+
+ this.usersApiClient = new UsersApiClient(config);
+ this.groupsApiClient = new GroupsApiClient(config);
+ }
+
+ public Collection create() {
+ ManifestFactory manifestFactory = ManifestFactory.builder()
+ .files(manifestFiles)
+ .locators(manifestLocators)
+ .build();
+ String manifest = manifestFactory.create();
+
+ Collection newCollection = new Collection();
+ newCollection.setName(getNameOrDefault(name));
+ newCollection.setManifestText(manifest);
+ newCollection.setOwnerUuid(getDesiredProjectUuid(projectUuid));
+
+ return newCollection;
+ }
+
+ private String getNameOrDefault(String name) {
+ return Optional.ofNullable(name).orElseGet(() -> {
+ LocalDateTime dateTime = LocalDateTime.now();
+ DateTimeFormatter formatter = DateTimeFormatter.ofPattern("Y-MM-dd HH:mm:ss.SSS");
+ return String.format("New Collection (%s)", dateTime.format(formatter));
+ });
+ }
+
+ public String getDesiredProjectUuid(String projectUuid) {
+ try {
+ if (projectUuid == null || projectUuid.length() == 0){
+ return usersApiClient.current().getUuid();
+ } else if (projectUuid.matches(Patterns.USER_UUID_PATTERN)) {
+ return usersApiClient.get(projectUuid).getUuid();
+ } else if (projectUuid.matches(Patterns.GROUP_UUID_PATTERN)) {
+ return groupsApiClient.get(projectUuid).getUuid();
+ }
+ } catch (ArvadosApiException e) {
+ throw new ArvadosClientException(String.format("An error occurred while getting project by UUID %s", projectUuid));
+ }
+ throw new ArvadosClientException(String.format("No project with %s UUID found", projectUuid));
+ }
+
+ public static class CollectionFactoryBuilder {
+ private ConfigProvider config;
+ private String name;
+ private String projectUuid;
+ private List<File> manifestFiles;
+ private List<String> manifestLocators;
+
+ CollectionFactoryBuilder() {
+ }
+
+ public CollectionFactoryBuilder config(ConfigProvider config) {
+ this.config = config;
+ return this;
+ }
+
+ public CollectionFactoryBuilder name(String name) {
+ this.name = name;
+ return this;
+ }
+
+ public CollectionFactoryBuilder projectUuid(String projectUuid) {
+ this.projectUuid = projectUuid;
+ return this;
+ }
+
+ public CollectionFactoryBuilder manifestFiles(List<File> manifestFiles) {
+ this.manifestFiles = manifestFiles;
+ return this;
+ }
+
+ public CollectionFactoryBuilder manifestLocators(List<String> manifestLocators) {
+ this.manifestLocators = manifestLocators;
+ return this;
+ }
+
+ public CollectionFactory build() {
+ return new CollectionFactory(config, name, projectUuid, manifestFiles, manifestLocators);
+ }
+
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+import com.google.common.base.Strings;
+import org.arvados.client.common.Characters;
+
+public class FileToken {
+
+ private int filePosition;
+ private int fileSize;
+ private String fileName;
+ private String path;
+
+ public FileToken(String fileTokenInfo) {
+ splitFileTokenInfo(fileTokenInfo);
+ }
+
+ public FileToken(String fileTokenInfo, String path) {
+ splitFileTokenInfo(fileTokenInfo);
+ this.path = path;
+ }
+
+ private void splitFileTokenInfo(String fileTokenInfo) {
+ String[] tokenPieces = fileTokenInfo.split(":");
+ this.filePosition = Integer.parseInt(tokenPieces[0]);
+ this.fileSize = Integer.parseInt(tokenPieces[1]);
+ this.fileName = tokenPieces[2].replace(Characters.SPACE, " ");
+ }
+
+ @Override
+ public String toString() {
+ return filePosition + ":" + fileSize + ":" + fileName;
+ }
+
+ public String getFullPath() {
+ return Strings.isNullOrEmpty(path) ? fileName : path + fileName;
+ }
+
+ public int getFilePosition() {
+ return this.filePosition;
+ }
+
+ public int getFileSize() {
+ return this.fileSize;
+ }
+
+ public String getFileName() {
+ return this.fileName;
+ }
+
+ public String getPath() {
+ return this.path;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+import org.arvados.client.common.Characters;
+import org.arvados.client.exception.ArvadosClientException;
+import org.arvados.client.logic.keep.KeepLocator;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Objects;
+
+import static java.util.stream.Collectors.toList;
+import static org.arvados.client.common.Patterns.FILE_TOKEN_PATTERN;
+import static org.arvados.client.common.Patterns.LOCATOR_PATTERN;
+
+public class ManifestDecoder {
+
+ public List<ManifestStream> decode(String manifestText) {
+
+ if (manifestText == null || manifestText.isEmpty()) {
+ throw new ArvadosClientException("Manifest text cannot be empty.");
+ }
+
+ List<String> manifestStreams = new ArrayList<>(Arrays.asList(manifestText.split("\\n")));
+ if (!manifestStreams.get(0).startsWith(". ")) {
+ throw new ArvadosClientException("Invalid first path component (expecting \".\")");
+ }
+
+ return manifestStreams.stream()
+ .map(this::decodeSingleManifestStream)
+ .collect(toList());
+ }
+
+ private ManifestStream decodeSingleManifestStream(String manifestStream) {
+ Objects.requireNonNull(manifestStream, "Manifest stream cannot be empty.");
+
+ LinkedList<String> manifestPieces = new LinkedList<>(Arrays.asList(manifestStream.split("\\s+")));
+ String streamName = manifestPieces.poll();
+ String path = ".".equals(streamName) ? "" : streamName.substring(2).concat(Characters.SLASH);
+
+ List<KeepLocator> keepLocators = manifestPieces
+ .stream()
+ .filter(p -> p.matches(LOCATOR_PATTERN))
+ .map(this::getKeepLocator)
+ .collect(toList());
+
+
+ List<FileToken> fileTokens = manifestPieces.stream()
+ .skip(keepLocators.size())
+ .filter(p -> p.matches(FILE_TOKEN_PATTERN))
+ .map(p -> new FileToken(p, path))
+ .collect(toList());
+
+ return new ManifestStream(streamName, keepLocators, fileTokens);
+
+ }
+
+ private KeepLocator getKeepLocator(String locatorString ) {
+ try {
+ return new KeepLocator(locatorString);
+ } catch (Exception e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+import com.google.common.collect.ImmutableList;
+import org.arvados.client.common.Characters;
+
+import java.io.File;
+import java.util.Collection;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class ManifestFactory {
+
+ private Collection<File> files;
+ private List<String> locators;
+
+ ManifestFactory(Collection<File> files, List<String> locators) {
+ this.files = files;
+ this.locators = locators;
+ }
+
+ public static ManifestFactoryBuilder builder() {
+ return new ManifestFactoryBuilder();
+ }
+
+ public String create() {
+ ImmutableList.Builder<String> builder = new ImmutableList.Builder<String>()
+ .add(Characters.DOT)
+ .addAll(locators);
+ long filePosition = 0;
+ for (File file : files) {
+ builder.add(String.format("%d:%d:%s", filePosition, file.length(), file.getName().replace(" ", Characters.SPACE)));
+ filePosition += file.length();
+ }
+ String manifest = builder.build().stream().collect(Collectors.joining(" ")).concat(Characters.NEW_LINE);
+ return manifest;
+ }
+
+ public static class ManifestFactoryBuilder {
+ private Collection<File> files;
+ private List<String> locators;
+
+ ManifestFactoryBuilder() {
+ }
+
+ public ManifestFactory.ManifestFactoryBuilder files(Collection<File> files) {
+ this.files = files;
+ return this;
+ }
+
+ public ManifestFactory.ManifestFactoryBuilder locators(List<String> locators) {
+ this.locators = locators;
+ return this;
+ }
+
+ public ManifestFactory build() {
+ return new ManifestFactory(files, locators);
+ }
+
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+import org.arvados.client.logic.keep.KeepLocator;
+
+import java.util.List;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public class ManifestStream {
+
+ private String streamName;
+ private List<KeepLocator> keepLocators;
+ private List<FileToken> fileTokens;
+
+ public ManifestStream(String streamName, List<KeepLocator> keepLocators, List<FileToken> fileTokens) {
+ this.streamName = streamName;
+ this.keepLocators = keepLocators;
+ this.fileTokens = fileTokens;
+ }
+
+ @Override
+ public String toString() {
+ return streamName + " " + Stream.concat(keepLocators.stream().map(KeepLocator::toString), fileTokens.stream().map(FileToken::toString))
+ .collect(Collectors.joining(" "));
+ }
+
+ public String getStreamName() {
+ return this.streamName;
+ }
+
+ public List<KeepLocator> getKeepLocators() {
+ return this.keepLocators;
+ }
+
+ public List<FileToken> getFileTokens() {
+ return this.fileTokens;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep;
+
+import com.google.common.collect.Lists;
+import org.arvados.client.api.client.CollectionsApiClient;
+import org.arvados.client.api.client.KeepWebApiClient;
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.common.Characters;
+import org.arvados.client.exception.ArvadosClientException;
+import org.arvados.client.logic.collection.FileToken;
+import org.arvados.client.logic.collection.ManifestDecoder;
+import org.arvados.client.logic.collection.ManifestStream;
+import org.arvados.client.logic.keep.exception.DownloadFolderAlreadyExistsException;
+import org.arvados.client.logic.keep.exception.FileAlreadyExistsException;
+import org.slf4j.Logger;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.CompletableFuture;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public class FileDownloader {
+
+ private final KeepClient keepClient;
+ private final ManifestDecoder manifestDecoder;
+ private final CollectionsApiClient collectionsApiClient;
+ private final KeepWebApiClient keepWebApiClient;
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(FileDownloader.class);
+
+ public FileDownloader(KeepClient keepClient, ManifestDecoder manifestDecoder, CollectionsApiClient collectionsApiClient, KeepWebApiClient keepWebApiClient) {
+ this.keepClient = keepClient;
+ this.manifestDecoder = manifestDecoder;
+ this.collectionsApiClient = collectionsApiClient;
+ this.keepWebApiClient = keepWebApiClient;
+ }
+
+ public List<FileToken> listFileInfoFromCollection(String collectionUuid) {
+ Collection requestedCollection = collectionsApiClient.get(collectionUuid);
+ String manifestText = requestedCollection.getManifestText();
+
+ // decode manifest text and get list of all FileTokens for this collection
+ return manifestDecoder.decode(manifestText)
+ .stream()
+ .flatMap(p -> p.getFileTokens().stream())
+ .collect(Collectors.toList());
+ }
+
+ public File downloadSingleFileUsingKeepWeb(String filePathName, String collectionUuid, String pathToDownloadFolder) {
+ FileToken fileToken = getFileTokenFromCollection(filePathName, collectionUuid);
+ if (fileToken == null) {
+ throw new ArvadosClientException(String.format("%s not found in Collection with UUID %s", filePathName, collectionUuid));
+ }
+
+ File downloadedFile = checkIfFileExistsInTargetLocation(fileToken, pathToDownloadFolder);
+ try (FileOutputStream fos = new FileOutputStream(downloadedFile)) {
+ fos.write(keepWebApiClient.download(collectionUuid, filePathName));
+ } catch (IOException e) {
+ throw new ArvadosClientException(String.format("Unable to write down file %s", fileToken.getFileName()), e);
+ }
+ return downloadedFile;
+ }
+
+ public List<File> downloadFilesFromCollectionUsingKeepWeb(String collectionUuid, String pathToDownloadFolder) {
+ String collectionTargetDir = setTargetDirectory(collectionUuid, pathToDownloadFolder).getAbsolutePath();
+ List<FileToken> fileTokens = listFileInfoFromCollection(collectionUuid);
+
+ List<CompletableFuture<File>> futures = Lists.newArrayList();
+ for (FileToken fileToken : fileTokens) {
+ futures.add(CompletableFuture.supplyAsync(() -> this.downloadOneFileFromCollectionUsingKeepWeb(fileToken, collectionUuid, collectionTargetDir)));
+ }
+
+ @SuppressWarnings("unchecked")
+ CompletableFuture<File>[] array = futures.toArray(new CompletableFuture[0]);
+ return Stream.of(array)
+ .map(CompletableFuture::join).collect(Collectors.toList());
+ }
+
+ private FileToken getFileTokenFromCollection(String filePathName, String collectionUuid) {
+ return listFileInfoFromCollection(collectionUuid)
+ .stream()
+ .filter(p -> (p.getFullPath()).equals(filePathName))
+ .findFirst()
+ .orElse(null);
+ }
+
+ private File checkIfFileExistsInTargetLocation(FileToken fileToken, String pathToDownloadFolder) {
+ String fileName = fileToken.getFileName();
+
+ File downloadFile = new File(pathToDownloadFolder + Characters.SLASH + fileName);
+ if (downloadFile.exists()) {
+ throw new FileAlreadyExistsException(String.format("File %s exists in location %s", fileName, pathToDownloadFolder));
+ } else {
+ return downloadFile;
+ }
+ }
+
+ private File downloadOneFileFromCollectionUsingKeepWeb(FileToken fileToken, String collectionUuid, String pathToDownloadFolder) {
+ String filePathName = fileToken.getPath() + fileToken.getFileName();
+ File downloadedFile = new File(pathToDownloadFolder + Characters.SLASH + filePathName);
+ downloadedFile.getParentFile().mkdirs();
+
+ try (FileOutputStream fos = new FileOutputStream(downloadedFile)) {
+ fos.write(keepWebApiClient.download(collectionUuid, filePathName));
+ } catch (IOException e) {
+ throw new RuntimeException(e);
+ }
+ return downloadedFile;
+ }
+
+ public List<File> downloadFilesFromCollection(String collectionUuid, String pathToDownloadFolder) {
+
+ // download requested collection and extract manifest text
+ Collection requestedCollection = collectionsApiClient.get(collectionUuid);
+ String manifestText = requestedCollection.getManifestText();
+
+ // if directory with this collectionUUID does not exist - create one
+ // if exists - abort (throw exception)
+ File collectionTargetDir = setTargetDirectory(collectionUuid, pathToDownloadFolder);
+
+ // decode manifest text and create list of ManifestStream objects containing KeepLocators and FileTokens
+ List<ManifestStream> manifestStreams = manifestDecoder.decode(manifestText);
+
+ //list of all downloaded files that will be returned by this method
+ List<File> downloadedFilesFromCollection = new ArrayList<>();
+
+ // download files for each manifest stream
+ for (ManifestStream manifestStream : manifestStreams)
+ downloadedFilesFromCollection.addAll(downloadFilesFromSingleManifestStream(manifestStream, collectionTargetDir));
+
+ log.debug(String.format("Total of: %d files downloaded", downloadedFilesFromCollection.size()));
+ return downloadedFilesFromCollection;
+ }
+
+ private File setTargetDirectory(String collectionUUID, String pathToDownloadFolder) {
+ //local directory to save downloaded files
+ File collectionTargetDir = new File(pathToDownloadFolder + Characters.SLASH + collectionUUID);
+ if (collectionTargetDir.exists()) {
+ throw new DownloadFolderAlreadyExistsException(String.format("Directory for collection UUID %s already exists", collectionUUID));
+ } else {
+ collectionTargetDir.mkdirs();
+ }
+ return collectionTargetDir;
+ }
+
+ private List<File> downloadFilesFromSingleManifestStream(ManifestStream manifestStream, File collectionTargetDir){
+ List<File> downloadedFiles = new ArrayList<>();
+ List<KeepLocator> keepLocators = manifestStream.getKeepLocators();
+ DownloadHelper downloadHelper = new DownloadHelper(keepLocators);
+
+ for (FileToken fileToken : manifestStream.getFileTokens()) {
+ File downloadedFile = new File(collectionTargetDir.getAbsolutePath() + Characters.SLASH + fileToken.getFullPath()); //create file
+ downloadedFile.getParentFile().mkdirs();
+
+ try (FileOutputStream fos = new FileOutputStream(downloadedFile, true)) {
+ downloadHelper.setBytesToDownload(fileToken.getFileSize()); //update file size info
+
+ //this part needs to be repeated for each file until whole file is downloaded
+ do {
+ downloadHelper.requestNewDataChunk(); //check if new data chunk needs to be downloaded
+ downloadHelper.writeDownFile(fos); // download data from chunk
+ } while (downloadHelper.getBytesToDownload() != 0);
+
+ } catch (IOException | ArvadosClientException e) {
+ throw new ArvadosClientException(String.format("Unable to write down file %s", fileToken.getFileName()), e);
+ }
+
+ downloadedFiles.add(downloadedFile);
+ log.debug(String.format("File %d / %d downloaded from manifest stream",
+ manifestStream.getFileTokens().indexOf(fileToken) + 1,
+ manifestStream.getFileTokens().size()));
+ }
+ return downloadedFiles;
+ }
+
+ private class DownloadHelper {
+
+ // values for tracking file output streams and matching data chunks with initial files
+ int currentDataChunkNumber;
+ int bytesDownloadedFromChunk;
+ int bytesToDownload;
+ byte[] currentDataChunk;
+ boolean remainingDataInChunk;
+ final List<KeepLocator> keepLocators;
+
+ private DownloadHelper(List<KeepLocator> keepLocators) {
+ currentDataChunkNumber = -1;
+ bytesDownloadedFromChunk = 0;
+ remainingDataInChunk = false;
+ this.keepLocators = keepLocators;
+ }
+
+ private int getBytesToDownload() {
+ return bytesToDownload;
+ }
+
+ private void setBytesToDownload(int bytesToDownload) {
+ this.bytesToDownload = bytesToDownload;
+ }
+
+ private void requestNewDataChunk() {
+ if (!remainingDataInChunk) {
+ currentDataChunkNumber++;
+ if (currentDataChunkNumber < keepLocators.size()) {
+ //swap data chunk for next one
+ currentDataChunk = keepClient.getDataChunk(keepLocators.get(currentDataChunkNumber));
+ log.debug(String.format("%d of %d data chunks from manifest stream downloaded", currentDataChunkNumber + 1, keepLocators.size()));
+ } else {
+ throw new ArvadosClientException("Data chunk required for download is missing.");
+ }
+ }
+ }
+
+ private void writeDownFile(FileOutputStream fos) throws IOException {
+ //case 1: more bytes needed than available in current chunk (or whole current chunk needed) to download file
+ if (bytesToDownload >= currentDataChunk.length - bytesDownloadedFromChunk) {
+ writeDownWholeDataChunk(fos);
+ }
+ //case 2: current data chunk contains more bytes than is needed for this file
+ else {
+ writeDownDataChunkPartially(fos);
+ }
+ }
+
+ private void writeDownWholeDataChunk(FileOutputStream fos) throws IOException {
+ // write all remaining bytes from current chunk
+ fos.write(currentDataChunk, bytesDownloadedFromChunk, currentDataChunk.length - bytesDownloadedFromChunk);
+ //update bytesToDownload
+ bytesToDownload -= (currentDataChunk.length - bytesDownloadedFromChunk);
+ // set remaining data in chunk to false
+ remainingDataInChunk = false;
+ //reset bytesDownloadedFromChunk so that its set to 0 for the next chunk
+ bytesDownloadedFromChunk = 0;
+ }
+
+ private void writeDownDataChunkPartially(FileOutputStream fos) throws IOException {
+ //write all remaining bytes for this file from current chunk
+ fos.write(currentDataChunk, bytesDownloadedFromChunk, bytesToDownload);
+ // update number of bytes downloaded from this chunk
+ bytesDownloadedFromChunk += bytesToDownload;
+ // set remaining data in chunk to true
+ remainingDataInChunk = true;
+ // reset bytesToDownload to exit while loop and move to the next file
+ bytesToDownload = 0;
+ }
+ }
+}
\ No newline at end of file
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep;
+
+import org.arvados.client.api.client.KeepServerApiClient;
+import org.arvados.client.exception.ArvadosApiException;
+import org.arvados.client.config.ConfigProvider;
+import org.slf4j.Logger;
+
+import java.io.File;
+import java.util.Map;
+
+public class FileTransferHandler {
+
+ private final String host;
+ private final KeepServerApiClient keepServerApiClient;
+ private final Map<String, String> headers;
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(FileTransferHandler.class);
+
+ public FileTransferHandler(String host, Map<String, String> headers, ConfigProvider config) {
+ this.host = host;
+ this.headers = headers;
+ this.keepServerApiClient = new KeepServerApiClient(config);
+ }
+
+ public String put(String hashString, File body) {
+ String url = host + hashString;
+ String locator = null;
+ try {
+ locator = keepServerApiClient.upload(url, headers, body);
+ } catch (ArvadosApiException e) {
+ log.error("Cannot upload file to Keep server.", e);
+ }
+ return locator;
+ }
+
+ public byte[] get(KeepLocator locator) {
+ return get(locator.stripped(), locator.permissionHint());
+ }
+
+ public byte[] get(String blockLocator, String authToken) {
+ String url = host + blockLocator + "+" + authToken;
+ try {
+ return keepServerApiClient.download(url);
+ } catch (ArvadosApiException e) {
+ log.error("Cannot download file from Keep server.", e);
+ return null;
+ }
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep;
+
+import com.google.common.collect.Lists;
+import org.arvados.client.api.client.CollectionsApiClient;
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.common.Characters;
+import org.arvados.client.config.ConfigProvider;
+import org.arvados.client.exception.ArvadosClientException;
+import org.arvados.client.logic.collection.CollectionFactory;
+import org.arvados.client.utils.FileMerge;
+import org.arvados.client.utils.FileSplit;
+import org.slf4j.Logger;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Objects;
+import java.util.UUID;
+
+import static java.util.stream.Collectors.toList;
+
+public class FileUploader {
+
+ private final KeepClient keepClient;
+ private final CollectionsApiClient collectionsApiClient;
+ private final ConfigProvider config;
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(FileUploader.class);
+
+ public FileUploader(KeepClient keepClient, CollectionsApiClient collectionsApiClient, ConfigProvider config) {
+ this.keepClient = keepClient;
+ this.collectionsApiClient = collectionsApiClient;
+ this.config = config;
+ }
+
+ public Collection upload(List<File> sourceFiles, String collectionName, String projectUuid) {
+ List<String> locators = uploadToKeep(sourceFiles);
+ CollectionFactory collectionFactory = CollectionFactory.builder()
+ .config(config)
+ .name(collectionName)
+ .projectUuid(projectUuid)
+ .manifestFiles(sourceFiles)
+ .manifestLocators(locators)
+ .build();
+
+ Collection newCollection = collectionFactory.create();
+ return collectionsApiClient.create(newCollection);
+ }
+
+ public Collection uploadToExistingCollection(List<File> files, String collectionUuid) {
+ List<String> locators = uploadToKeep(files);
+ Collection collectionBeforeUpload = collectionsApiClient.get(collectionUuid);
+ String oldManifest = collectionBeforeUpload.getManifestText();
+
+ CollectionFactory collectionFactory = CollectionFactory.builder()
+ .config(config)
+ .manifestFiles(files)
+ .manifestLocators(locators).build();
+
+ String newPartOfManifestText = collectionFactory.create().getManifestText();
+ String newManifest = oldManifest + newPartOfManifestText;
+
+ collectionBeforeUpload.setManifestText(newManifest);
+ return collectionsApiClient.update(collectionBeforeUpload);
+ }
+
+ private List<String> uploadToKeep(List<File> files) {
+ File targetDir = config.getFileSplitDirectory();
+ File combinedFile = new File(targetDir.getAbsolutePath() + Characters.SLASH + UUID.randomUUID());
+ List<File> chunks;
+ try {
+ FileMerge.merge(files, combinedFile);
+ chunks = FileSplit.split(combinedFile, targetDir, config.getFileSplitSize());
+ } catch (IOException e) {
+ throw new ArvadosClientException("Cannot create file chunks for upload", e);
+ }
+ combinedFile.delete();
+
+ int copies = config.getNumberOfCopies();
+ int numRetries = config.getNumberOfRetries();
+
+ List<String> locators = Lists.newArrayList();
+ for (File chunk : chunks) {
+ try {
+ locators.add(keepClient.put(chunk, copies, numRetries));
+ } catch (ArvadosClientException e) {
+ log.error("Problem occurred while uploading chunk file {}", chunk.getName(), e);
+ throw e;
+ }
+ }
+ return locators.stream()
+ .filter(Objects::nonNull)
+ .collect(toList());
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep;
+
+import com.google.common.collect.Lists;
+import org.apache.commons.codec.digest.DigestUtils;
+import org.apache.commons.io.FileUtils;
+import org.arvados.client.api.client.KeepServicesApiClient;
+import org.arvados.client.api.model.KeepService;
+import org.arvados.client.api.model.KeepServiceList;
+import org.arvados.client.common.Characters;
+import org.arvados.client.common.Headers;
+import org.arvados.client.config.ConfigProvider;
+import org.arvados.client.exception.ArvadosApiException;
+import org.arvados.client.exception.ArvadosClientException;
+import org.slf4j.Logger;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.concurrent.CompletableFuture;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public class KeepClient {
+
+ private final KeepServicesApiClient keepServicesApiClient;
+ private final Logger log = org.slf4j.LoggerFactory.getLogger(KeepClient.class);
+ private List<KeepService> keepServices;
+ private List<KeepService> writableServices;
+ private Map<String, KeepService> gatewayServices;
+ private final String apiToken;
+ private Integer maxReplicasPerService;
+ private final ConfigProvider config;
+
+ public KeepClient(ConfigProvider config) {
+ this.config = config;
+ keepServicesApiClient = new KeepServicesApiClient(config);
+ apiToken = config.getApiToken();
+ }
+
+ public byte[] getDataChunk(KeepLocator keepLocator) {
+
+ Map<String, String> headers = new HashMap<>();
+ Map<String, FileTransferHandler> rootsMap = new HashMap<>();
+
+ List<String> sortedRoots = mapNewServices(rootsMap, keepLocator, false, false, headers);
+
+ byte[] dataChunk = sortedRoots
+ .stream()
+ .map(rootsMap::get)
+ .map(r -> r.get(keepLocator))
+ .filter(Objects::nonNull)
+ .findFirst()
+ .orElse(null);
+
+ if (dataChunk == null) {
+ throw new ArvadosClientException("No server responding. Unable to download data chunk.");
+ }
+
+ return dataChunk;
+ }
+
+ public String put(File data, int copies, int numRetries) {
+
+ byte[] fileBytes;
+ try {
+ fileBytes = FileUtils.readFileToByteArray(data);
+ } catch (IOException e) {
+ throw new ArvadosClientException("An error occurred while reading data chunk", e);
+ }
+
+ String dataHash = DigestUtils.md5Hex(fileBytes);
+ String locatorString = String.format("%s+%d", dataHash, data.length());
+
+ if (copies < 1) {
+ return locatorString;
+ }
+ KeepLocator locator = new KeepLocator(locatorString);
+
+ // Tell the proxy how many copies we want it to store
+ Map<String, String> headers = new HashMap<>();
+ headers.put(Headers.X_KEEP_DESIRED_REPLICAS, String.valueOf(copies));
+
+ Map<String, FileTransferHandler> rootsMap = new HashMap<>();
+ List<String> sortedRoots = mapNewServices(rootsMap, locator, false, true, headers);
+
+ int numThreads = 0;
+ if (maxReplicasPerService == null || maxReplicasPerService >= copies) {
+ numThreads = 1;
+ } else {
+ numThreads = ((Double) Math.ceil(1.0 * copies / maxReplicasPerService)).intValue();
+ }
+ log.debug("Pool max threads is {}", numThreads);
+
+ List<CompletableFuture<String>> futures = Lists.newArrayList();
+ for (int i = 0; i < numThreads; i++) {
+ String root = sortedRoots.get(i);
+ FileTransferHandler keepServiceLocal = rootsMap.get(root);
+ futures.add(CompletableFuture.supplyAsync(() -> keepServiceLocal.put(dataHash, data)));
+ }
+
+ @SuppressWarnings("unchecked")
+ CompletableFuture<String>[] array = futures.toArray(new CompletableFuture[0]);
+
+ return Stream.of(array)
+ .map(CompletableFuture::join)
+ .reduce((a, b) -> b)
+ .orElse(null);
+ }
+
+ private List<String> mapNewServices(Map<String, FileTransferHandler> rootsMap, KeepLocator locator,
+ boolean forceRebuild, boolean needWritable, Map<String, String> headers) {
+
+ headers.putIfAbsent("Authorization", String.format("OAuth2 %s", apiToken));
+ List<String> localRoots = weightedServiceRoots(locator, forceRebuild, needWritable);
+ for (String root : localRoots) {
+ FileTransferHandler keepServiceLocal = new FileTransferHandler(root, headers, config);
+ rootsMap.putIfAbsent(root, keepServiceLocal);
+ }
+ return localRoots;
+ }
+
+ /**
+ * Return an array of Keep service endpoints, in the order in which they should be probed when reading or writing
+ * data with the given hash+hints.
+ */
+ private List<String> weightedServiceRoots(KeepLocator locator, boolean forceRebuild, boolean needWritable) {
+
+ buildServicesList(forceRebuild);
+
+ List<String> sortedRoots = new ArrayList<>();
+
+ // Use the services indicated by the given +K@... remote
+ // service hints, if any are present and can be resolved to a
+ // URI.
+ //
+ for (String hint : locator.getHints()) {
+ if (hint.startsWith("K@")) {
+ if (hint.length() == 7) {
+ sortedRoots.add(String.format("https://keep.%s.arvadosapi.com/", hint.substring(2)));
+ } else if (hint.length() == 29) {
+ KeepService svc = gatewayServices.get(hint.substring(2));
+ if (svc != null) {
+ sortedRoots.add(svc.getServiceRoot());
+ }
+ }
+ }
+ }
+
+ // Sort the available local services by weight (heaviest first)
+ // for this locator, and return their service_roots (base URIs)
+ // in that order.
+ List<KeepService> useServices = keepServices;
+ if (needWritable) {
+ useServices = writableServices;
+ }
+ anyNonDiskServices(useServices);
+
+ sortedRoots.addAll(useServices
+ .stream()
+ .sorted((ks1, ks2) -> serviceWeight(locator.getMd5sum(), ks2.getUuid())
+ .compareTo(serviceWeight(locator.getMd5sum(), ks1.getUuid())))
+ .map(KeepService::getServiceRoot)
+ .collect(Collectors.toList()));
+
+ return sortedRoots;
+ }
+
+ private void buildServicesList(boolean forceRebuild) {
+ if (keepServices != null && !forceRebuild) {
+ return;
+ }
+ KeepServiceList keepServiceList;
+ try {
+ keepServiceList = keepServicesApiClient.accessible();
+ } catch (ArvadosApiException e) {
+ throw new ArvadosClientException("Cannot obtain list of accessible keep services");
+ }
+ // Gateway services are only used when specified by UUID,
+ // so there's nothing to gain by filtering them by
+ // service_type.
+ gatewayServices = keepServiceList.getItems().stream().collect(Collectors.toMap(KeepService::getUuid, Function.identity()));
+
+ if (gatewayServices.isEmpty()) {
+ throw new ArvadosClientException("No gateway services available!");
+ }
+
+ // Precompute the base URI for each service.
+ for (KeepService keepService : gatewayServices.values()) {
+ String serviceHost = keepService.getServiceHost();
+ if (!serviceHost.startsWith("[") && serviceHost.contains(Characters.COLON)) {
+ // IPv6 URIs must be formatted like http://[::1]:80/...
+ serviceHost = String.format("[%s]", serviceHost);
+ }
+
+ String protocol = keepService.getServiceSslFlag() ? "https" : "http";
+ String serviceRoot = String.format("%s://%s:%d/", protocol, serviceHost, keepService.getServicePort());
+ keepService.setServiceRoot(serviceRoot);
+ }
+
+ keepServices = gatewayServices.values().stream().filter(ks -> !ks.getServiceType().startsWith("gateway:")).collect(Collectors.toList());
+ writableServices = keepServices.stream().filter(ks -> !ks.getReadOnly()).collect(Collectors.toList());
+
+ // For disk type services, max_replicas_per_service is 1
+ // It is unknown (unlimited) for other service types.
+ if (anyNonDiskServices(writableServices)) {
+ maxReplicasPerService = null;
+ } else {
+ maxReplicasPerService = 1;
+ }
+ }
+
+ private Boolean anyNonDiskServices(List<KeepService> useServices) {
+ return useServices.stream().anyMatch(ks -> !ks.getServiceType().equals("disk"));
+ }
+
+ /**
+ * Compute the weight of a Keep service endpoint for a data block with a known hash.
+ * <p>
+ * The weight is md5(h + u) where u is the last 15 characters of the service endpoint's UUID.
+ */
+ private static String serviceWeight(String dataHash, String serviceUuid) {
+ String shortenedUuid;
+ if (serviceUuid != null && serviceUuid.length() >= 15) {
+ int substringIndex = serviceUuid.length() - 15;
+ shortenedUuid = serviceUuid.substring(substringIndex);
+ } else {
+ shortenedUuid = (serviceUuid == null) ? "" : serviceUuid;
+ }
+ return DigestUtils.md5Hex(dataHash + shortenedUuid);
+ }
+
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep;
+
+import org.arvados.client.exception.ArvadosClientException;
+
+import java.time.Instant;
+import java.time.LocalDateTime;
+import java.time.ZoneOffset;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static org.arvados.client.common.Patterns.HINT_PATTERN;
+
+public class KeepLocator {
+
+ private final List<String> hints = new ArrayList<>();
+ private String permSig;
+ private LocalDateTime permExpiry;
+ private final String md5sum;
+ private final Integer size;
+
+ public KeepLocator(String locatorString) {
+ LinkedList<String> pieces = new LinkedList<>(Arrays.asList(locatorString.split("\\+")));
+
+ md5sum = pieces.poll();
+ size = Integer.valueOf(Objects.requireNonNull(pieces.poll()));
+
+ for (String hint : pieces) {
+ if (!hint.matches(HINT_PATTERN)) {
+ throw new ArvadosClientException(String.format("invalid hint format: %s", hint));
+ } else if (hint.startsWith("A")) {
+ parsePermissionHint(hint);
+ } else {
+ hints.add(hint);
+ }
+ }
+ }
+
+ public List<String> getHints() {
+ return hints;
+ }
+
+ public String getMd5sum() {
+ return md5sum;
+ }
+
+ @Override
+ public String toString() {
+ return Stream.concat(Stream.of(md5sum, size.toString(), permissionHint()), hints.stream())
+ .filter(Objects::nonNull)
+ .collect(Collectors.joining("+"));
+ }
+
+ public String stripped() {
+ return size != null ? String.format("%s+%d", md5sum, size) : md5sum;
+ }
+
+ public String permissionHint() {
+ if (permSig == null || permExpiry == null) {
+ return null;
+ }
+
+ long timestamp = permExpiry.toEpochSecond(ZoneOffset.UTC);
+ String signTimestamp = Long.toHexString(timestamp);
+ return String.format("A%s@%s", permSig, signTimestamp);
+ }
+
+ private void parsePermissionHint(String hint) {
+ String[] hintSplit = hint.substring(1).split("@", 2);
+ permSig = hintSplit[0];
+
+ int permExpiryDecimal = Integer.parseInt(hintSplit[1], 16);
+ permExpiry = LocalDateTime.ofInstant(Instant.ofEpochSecond(permExpiryDecimal), ZoneOffset.UTC);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep.exception;
+
+import org.arvados.client.exception.ArvadosClientException;
+
+/**
+ * Exception indicating that directory with given name was already created in specified location.
+ *
+ * <p> This exception will be thrown during an attempt to download all files from certain
+ * collection to a location that already contains folder named by this collection's UUID.</p>
+ */
+public class DownloadFolderAlreadyExistsException extends ArvadosClientException {
+
+ public DownloadFolderAlreadyExistsException(String message) {
+ super(message);
+ }
+
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep.exception;
+
+import org.arvados.client.exception.ArvadosClientException;
+
+/**
+ * Signals that an attempt to download a file with given name has failed for a specified
+ * download location.
+ *
+ * <p> This exception will be thrown during an attempt to download single file to a location
+ * that already contains file with given name</p>
+ */
+public class FileAlreadyExistsException extends ArvadosClientException {
+
+ public FileAlreadyExistsException(String message) { super(message); }
+
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.utils;
+
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.util.Collection;
+
+public class FileMerge {
+
+ public static void merge(Collection<File> files, File targetFile) throws IOException {
+ try (FileOutputStream fos = new FileOutputStream(targetFile); BufferedOutputStream mergingStream = new BufferedOutputStream(fos)) {
+ for (File file : files) {
+ Files.copy(file.toPath(), mergingStream);
+ }
+ }
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.utils;
+
+import org.apache.commons.io.FileUtils;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Based on:
+ * {@link} https://stackoverflow.com/questions/10864317/how-to-break-a-file-into-pieces-using-java
+ */
+public class FileSplit {
+
+ public static List<File> split(File f, File dir, int splitSize) throws IOException {
+ int partCounter = 1;
+
+ long sizeOfFiles = splitSize * FileUtils.ONE_MB;
+ byte[] buffer = new byte[(int) sizeOfFiles];
+
+ List<File> files = new ArrayList<>();
+ String fileName = f.getName();
+
+ try (FileInputStream fis = new FileInputStream(f); BufferedInputStream bis = new BufferedInputStream(fis)) {
+ int bytesAmount = 0;
+ while ((bytesAmount = bis.read(buffer)) > 0) {
+ String filePartName = String.format("%s.%03d", fileName, partCounter++);
+ File newFile = new File(dir, filePartName);
+ try (FileOutputStream out = new FileOutputStream(newFile)) {
+ out.write(buffer, 0, bytesAmount);
+ }
+ files.add(newFile);
+ }
+ }
+ return files;
+ }
+}
\ No newline at end of file
--- /dev/null
+# Arvados client default configuration
+#
+# Remarks:
+# * While providing data remove apostrophes ("") from each line
+# * See Arvados documentation for information how to obtain a token:
+# https://doc.arvados.org/user/reference/api-tokens.html
+#
+
+arvados {
+ api {
+ keepweb-host = localhost
+ keepweb-port = 8000
+ host = localhost
+ port = 8000
+ token = ""
+ protocol = https
+ host-insecure = false
+ }
+ split-size = 64
+ temp-dir = /tmp/file-split
+ copies = 2
+ retries = 0
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.HttpUrl;
+import org.arvados.client.api.model.Item;
+import org.arvados.client.api.model.ItemList;
+import org.arvados.client.test.utils.ArvadosClientUnitTest;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.Spy;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+@RunWith(MockitoJUnitRunner.class)
+public class BaseStandardApiClientTest extends ArvadosClientUnitTest {
+
+ @Spy
+ private BaseStandardApiClient<?, ?> client = new BaseStandardApiClient<Item, ItemList>(CONFIG) {
+ @Override
+ String getResource() {
+ return "resource";
+ }
+
+ @Override
+ Class<Item> getType() {
+ return null;
+ }
+
+ @Override
+ Class<ItemList> getListType() {
+ return null;
+ }
+ };
+
+ @Test
+ public void urlBuilderBuildsExpectedUrlFormat() {
+ // when
+ HttpUrl.Builder actual = client.getUrlBuilder();
+
+ // then
+ assertThat(actual.build().toString()).isEqualTo("http://localhost:9000/arvados/v1/resource");
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.mockwebserver.RecordedRequest;
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.api.model.CollectionList;
+import org.arvados.client.test.utils.RequestMethod;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.junit.Test;
+
+import static org.arvados.client.test.utils.ApiClientTestUtils.*;
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class CollectionsApiClientTest extends ArvadosClientMockedWebServerTest {
+
+ private static final String RESOURCE = "collections";
+
+ private CollectionsApiClient client = new CollectionsApiClient(CONFIG);
+
+ @Test
+ public void listCollections() throws Exception {
+
+ // given
+ server.enqueue(getResponse("collections-list"));
+
+ // when
+ CollectionList actual = client.list();
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertThat(actual.getItemsAvailable()).isEqualTo(41);
+ }
+
+ @Test
+ public void getCollection() throws Exception {
+
+ // given
+ server.enqueue(getResponse("collections-get"));
+
+ String uuid = "112ci-4zz18-p51w7z3fpopo6sm";
+
+ // when
+ Collection actual = client.get(uuid);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + "/" + uuid);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertThat(actual.getUuid()).isEqualTo(uuid);
+ assertThat(actual.getPortableDataHash()).isEqualTo("6c4106229b08fe25f48b3a7a8289dd46+143");
+ }
+
+ @Test
+ public void createCollection() throws Exception {
+
+ // given
+ server.enqueue(getResponse("collections-create-simple"));
+
+ String name = "Super Collection";
+
+ Collection collection = new Collection();
+ collection.setName(name);
+
+ // when
+ Collection actual = client.create(collection);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+ assertRequestMethod(request, RequestMethod.POST);
+ assertThat(actual.getName()).isEqualTo(name);
+ assertThat(actual.getPortableDataHash()).isEqualTo("d41d8cd98f00b204e9800998ecf8427e+0");
+ assertThat(actual.getManifestText()).isEmpty();
+ }
+
+ @Test
+ public void createCollectionWithManifest() throws Exception {
+
+ // given
+ server.enqueue(getResponse("collections-create-manifest"));
+
+ String name = "Super Collection";
+ String manifestText = ". 7df44272090cee6c0732382bba415ee9+70+Aa5ece4560e3329315165b36c239b8ab79c888f8a@5a1d5708 0:70:README.md\n";
+
+ Collection collection = new Collection();
+ collection.setName(name);
+ collection.setManifestText(manifestText);
+
+ // when
+ Collection actual = client.create(collection);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+ assertRequestMethod(request, RequestMethod.POST);
+ assertThat(actual.getName()).isEqualTo(name);
+ assertThat(actual.getPortableDataHash()).isEqualTo("d41d8cd98f00b204e9800998ecf8427e+0");
+ assertThat(actual.getManifestText()).isEqualTo(manifestText);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import com.google.common.collect.Lists;
+import okhttp3.mockwebserver.RecordedRequest;
+import org.arvados.client.api.model.Group;
+import org.arvados.client.api.model.GroupList;
+import org.arvados.client.api.model.argument.Filter;
+import org.arvados.client.api.model.argument.ListArgument;
+import org.arvados.client.test.utils.RequestMethod;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+
+import static org.arvados.client.test.utils.ApiClientTestUtils.*;
+import static org.junit.Assert.assertEquals;
+
+public class GroupsApiClientTest extends ArvadosClientMockedWebServerTest {
+ private static final String RESOURCE = "groups";
+ private GroupsApiClient client = new GroupsApiClient(CONFIG);
+
+ @Test
+ public void listGroups() throws Exception {
+
+ // given
+ server.enqueue(getResponse("groups-list"));
+
+ // when
+ GroupList actual = client.list();
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertEquals(20, actual.getItems().size());
+ }
+
+ @Test
+ public void listProjectsByOwner() throws Exception {
+
+ // given
+ server.enqueue(getResponse("groups-list"));
+ String ownerUuid = "ardev-tpzed-n3kzq4fvoks3uw4";
+ String filterSubPath = "?filters=[%20[%20%22owner_uuid%22,%20%22like%22,%20%22ardev-tpzed-n3kzq4fvoks3uw4%22%20],%20" +
+ "[%20%22group_class%22,%20%22in%22,%20[%20%22project%22,%20%22sub-project%22%20]%20]%20]";
+
+ // when
+ ListArgument listArgument = ListArgument.builder()
+ .filters(Arrays.asList(
+ Filter.of("owner_uuid", Filter.Operator.LIKE, ownerUuid),
+ Filter.of("group_class", Filter.Operator.IN, Lists.newArrayList("project", "sub-project")
+ )))
+ .build();
+ GroupList actual = client.list(listArgument);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + filterSubPath);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertEquals(20, actual.getItems().size());
+ }
+
+ @Test
+ public void getGroup() throws Exception {
+
+ // given
+ server.enqueue(getResponse("groups-get"));
+
+ String uuid = "ardev-j7d0g-bmg3pfqtx3ivczp";
+
+ // when
+ Group actual = client.get(uuid);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + "/" + uuid);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertEquals(uuid, actual.getUuid());
+ assertEquals("3hw0vk4mbl0ofvia5k6x4dwrx", actual.getEtag());
+ assertEquals("ardev-tpzed-n3kzq4fvoks3uw4", actual.getOwnerUuid());
+ assertEquals("TestGroup1", actual.getName());
+ assertEquals("project", actual.getGroupClass());
+
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import com.google.common.collect.Maps;
+import okhttp3.mockwebserver.MockResponse;
+import okhttp3.mockwebserver.RecordedRequest;
+import okio.Buffer;
+import org.apache.commons.io.FileUtils;
+import org.arvados.client.common.Headers;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.Map;
+
+import static org.arvados.client.test.utils.ApiClientTestUtils.assertAuthorizationHeader;
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class KeepServerApiClientTest extends ArvadosClientMockedWebServerTest {
+
+ private KeepServerApiClient client = new KeepServerApiClient(CONFIG);
+
+ @Test
+ public void uploadFileToServer() throws Exception {
+
+ // given
+ String blockLocator = "7df44272090cee6c0732382bba415ee9";
+ String signedBlockLocator = blockLocator + "+70+A189a93acda6e1fba18a9dffd42b6591cbd36d55d@5a1c17b6";
+ server.enqueue(new MockResponse().setBody(signedBlockLocator));
+
+ String url = server.url(blockLocator).toString();
+ File body = new File("README.md");
+ Map<String, String> headers = Maps.newHashMap();
+ headers.put(Headers.X_KEEP_DESIRED_REPLICAS, "2");
+
+ // when
+ String actual = client.upload(url, headers, body);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertThat(request.getPath()).isEqualTo("/" + blockLocator);
+
+ assertThat(actual).isEqualTo(signedBlockLocator);
+ }
+
+ @Test
+ public void downloadFileFromServer() throws Exception {
+ File data = new File("README.md");
+ byte[] fileBytes = FileUtils.readFileToByteArray(data);
+ server.enqueue(new MockResponse().setBody(new Buffer().write(fileBytes)));
+
+ String blockLocator = "7df44272090cee6c0732382bba415ee9";
+ String signedBlockLocator = blockLocator + "+70+A189a93acda6e1fba18a9dffd42b6591cbd36d55d@5a1c17b6";
+
+ String url = server.url(signedBlockLocator).toString();
+
+ byte[] actual = client.download(url);
+ RecordedRequest request = server.takeRequest();
+ assertThat(request.getPath()).isEqualTo("/" + signedBlockLocator);
+ assertThat(actual).isEqualTo(fileBytes);
+
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.mockwebserver.RecordedRequest;
+import org.arvados.client.api.model.KeepService;
+import org.arvados.client.api.model.KeepServiceList;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.junit.Test;
+
+import static org.arvados.client.test.utils.ApiClientTestUtils.*;
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class KeepServicesApiClientTest extends ArvadosClientMockedWebServerTest {
+
+ private static final String RESOURCE = "keep_services";
+
+ private KeepServicesApiClient client = new KeepServicesApiClient(CONFIG);
+
+ @Test
+ public void listKeepServices() throws Exception {
+
+ // given
+ server.enqueue(getResponse("keep-services-list"));
+
+ // when
+ KeepServiceList actual = client.list();
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+
+ assertThat(actual.getItemsAvailable()).isEqualTo(3);
+
+ }
+
+ @Test
+ public void listAccessibleKeepServices() throws Exception {
+
+ // given
+ server.enqueue(getResponse("keep-services-accessible"));
+
+ // when
+ KeepServiceList actual = client.accessible();
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + "/accessible");
+ assertThat(actual.getItemsAvailable()).isEqualTo(2);
+ }
+
+ @Test
+ public void getKeepService() throws Exception {
+
+ // given
+ server.enqueue(getResponse("keep-services-get"));
+
+ String uuid = "112ci-bi6l4-hv02fg8sbti8ykk";
+
+ // whenFs
+ KeepService actual = client.get(uuid);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + "/" + uuid);
+ assertThat(actual.getUuid()).isEqualTo(uuid);
+ assertThat(actual.getServiceType()).isEqualTo("disk");
+ }
+
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.mockwebserver.RecordedRequest;
+import org.arvados.client.api.model.User;
+import org.arvados.client.api.model.UserList;
+import org.arvados.client.test.utils.RequestMethod;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.junit.Test;
+
+import static org.arvados.client.common.Characters.SLASH;
+import static org.arvados.client.test.utils.ApiClientTestUtils.*;
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class UsersApiClientTest extends ArvadosClientMockedWebServerTest {
+
+ private static final String RESOURCE = "users";
+ private static final String USER_UUID = "ardev-tpzed-q6dvn7sby55up1b";
+
+ private UsersApiClient client = new UsersApiClient(CONFIG);
+
+ @Test
+ public void listUsers() throws Exception {
+
+ // given
+ server.enqueue(getResponse("users-list"));
+
+ // when
+ UserList actual = client.list();
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertThat(actual.getItemsAvailable()).isEqualTo(13);
+ }
+
+ @Test
+ public void getUser() throws Exception {
+
+ // given
+ server.enqueue(getResponse("users-get"));
+
+ // when
+ User actual = client.get(USER_UUID);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + SLASH + USER_UUID);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertThat(actual.getUuid()).isEqualTo(USER_UUID);
+ }
+
+ @Test
+ public void getCurrentUser() throws Exception {
+
+ // given
+ server.enqueue(getResponse("users-get"));
+
+ // when
+ User actual = client.current();
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + SLASH + "current");
+ assertRequestMethod(request, RequestMethod.GET);
+ assertThat(actual.getUuid()).isEqualTo(USER_UUID);
+ }
+
+ @Test
+ public void getSystemUser() throws Exception {
+
+ // given
+ server.enqueue(getResponse("users-system"));
+
+ // when
+ User actual = client.system();
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + SLASH + "system");
+ assertRequestMethod(request, RequestMethod.GET);
+ assertThat(actual.getUuid()).isEqualTo("ardev-tpzed-000000000000000");
+ }
+
+ @Test
+ public void createUser() throws Exception {
+
+ // given
+ server.enqueue(getResponse("users-create"));
+
+ String firstName = "John";
+ String lastName = "Wayne";
+ String fullName = String.format("%s %s", firstName, lastName);
+ String username = String.format("%s%s", firstName, lastName).toLowerCase();
+
+ User user = new User();
+ user.setFirstName(firstName);
+ user.setLastName(lastName);
+ user.setFullName(fullName);
+ user.setUsername(username);
+
+ // when
+ User actual = client.create(user);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+ assertRequestMethod(request, RequestMethod.POST);
+ assertThat(actual.getFirstName()).isEqualTo(firstName);
+ assertThat(actual.getLastName()).isEqualTo(lastName);
+ assertThat(actual.getFullName()).isEqualTo(fullName);
+ assertThat(actual.getUsername()).isEqualTo(username);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client.factory;
+
+import okhttp3.OkHttpClient;
+import okhttp3.Request;
+import okhttp3.Response;
+import okhttp3.mockwebserver.MockResponse;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.junit.Assert;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import javax.net.ssl.KeyManagerFactory;
+import javax.net.ssl.SSLContext;
+import javax.net.ssl.SSLSocketFactory;
+import javax.net.ssl.TrustManagerFactory;
+import java.io.FileInputStream;
+import java.security.KeyStore;
+
+
+@RunWith(MockitoJUnitRunner.class)
+public class OkHttpClientFactoryTest extends ArvadosClientMockedWebServerTest {
+
+ @Test(expected = javax.net.ssl.SSLHandshakeException.class)
+ public void secureOkHttpClientIsCreated() throws Exception {
+
+ // given
+ OkHttpClientFactory factory = OkHttpClientFactory.builder().build();
+ // * configure HTTPS server
+ SSLSocketFactory sf = getSSLSocketFactoryWithSelfSignedCertificate();
+ server.useHttps(sf, false);
+ server.enqueue(new MockResponse().setBody("OK"));
+ // * prepare client HTTP request
+ Request request = new Request.Builder()
+ .url("https://localhost:9000/")
+ .build();
+
+ // when - then (SSL certificate is verified)
+ OkHttpClient actual = factory.create(false);
+ Response response = actual.newCall(request).execute();
+ }
+
+ @Test
+ public void insecureOkHttpClientIsCreated() throws Exception {
+ // given
+ OkHttpClientFactory factory = OkHttpClientFactory.builder().build();
+ // * configure HTTPS server
+ SSLSocketFactory sf = getSSLSocketFactoryWithSelfSignedCertificate();
+ server.useHttps(sf, false);
+ server.enqueue(new MockResponse().setBody("OK"));
+ // * prepare client HTTP request
+ Request request = new Request.Builder()
+ .url("https://localhost:9000/")
+ .build();
+
+ // when (SSL certificate is not verified)
+ OkHttpClient actual = factory.create(true);
+ Response response = actual.newCall(request).execute();
+
+ // then
+ Assert.assertEquals(response.body().string(),"OK");
+ }
+
+
+ /*
+ This ugly boilerplate is needed to enable self signed certificate.
+
+ It requires selfsigned.keystore.jks file. It was generated with:
+ keytool -genkey -v -keystore mystore.keystore.jks -alias alias_name -keyalg RSA -keysize 2048 -validity 10000
+ */
+ public SSLSocketFactory getSSLSocketFactoryWithSelfSignedCertificate() throws Exception {
+
+ FileInputStream stream = new FileInputStream("src/test/resources/selfsigned.keystore.jks");
+ char[] serverKeyStorePassword = "123456".toCharArray();
+ KeyStore serverKeyStore = KeyStore.getInstance(KeyStore.getDefaultType());
+ serverKeyStore.load(stream, serverKeyStorePassword);
+
+ String kmfAlgorithm = KeyManagerFactory.getDefaultAlgorithm();
+ KeyManagerFactory kmf = KeyManagerFactory.getInstance(kmfAlgorithm);
+ kmf.init(serverKeyStore, serverKeyStorePassword);
+
+ TrustManagerFactory trustManagerFactory = TrustManagerFactory.getInstance(kmfAlgorithm);
+ trustManagerFactory.init(serverKeyStore);
+
+ SSLContext sslContext = SSLContext.getInstance("SSL");
+ sslContext.init(kmf.getKeyManagers(), trustManagerFactory.getTrustManagers(), null);
+ return sslContext.getSocketFactory();
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.facade;
+
+import org.apache.commons.io.FileUtils;
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.common.Characters;
+import org.arvados.client.config.ExternalConfigProvider;
+import org.arvados.client.junit.categories.IntegrationTests;
+import org.arvados.client.logic.collection.FileToken;
+import org.arvados.client.test.utils.ArvadosClientIntegrationTest;
+import org.arvados.client.test.utils.FileTestUtils;
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+
+import java.io.File;
+import java.util.Collections;
+import java.util.List;
+import java.util.UUID;
+
+import static org.arvados.client.test.utils.FileTestUtils.FILE_DOWNLOAD_TEST_DIR;
+import static org.arvados.client.test.utils.FileTestUtils.FILE_SPLIT_TEST_DIR;
+import static org.arvados.client.test.utils.FileTestUtils.TEST_FILE;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+@Category(IntegrationTests.class)
+public class ArvadosFacadeIntegrationTest extends ArvadosClientIntegrationTest {
+
+
+ private static final String COLLECTION_NAME = "Test collection " + UUID.randomUUID().toString();
+ private String collectionUuid;
+
+ @Before
+ public void setUp() throws Exception {
+ FileTestUtils.createDirectory(FILE_SPLIT_TEST_DIR);
+ FileTestUtils.createDirectory(FILE_DOWNLOAD_TEST_DIR);
+ }
+
+ @Test
+ public void uploadOfFileIsPerformedSuccessfully() throws Exception {
+ // given
+ File file = FileTestUtils.generateFile(TEST_FILE, FileTestUtils.ONE_FOURTH_GB / 200);
+
+ // when
+ Collection actual = FACADE.upload(Collections.singletonList(file), COLLECTION_NAME, PROJECT_UUID);
+ collectionUuid = actual.getUuid();
+
+ // then
+ assertThat(actual.getName()).contains("Test collection");
+ assertThat(actual.getManifestText()).contains(file.length() + Characters.COLON + file.getName());
+ }
+
+ @Test
+ public void uploadOfFilesIsPerformedSuccessfully() throws Exception {
+ // given
+ List<File> files = FileTestUtils.generatePredefinedFiles();
+ files.addAll(FileTestUtils.generatePredefinedFiles());
+
+ // when
+ Collection actual = FACADE.upload(files, COLLECTION_NAME, PROJECT_UUID);
+ collectionUuid = actual.getUuid();
+
+ // then
+ assertThat(actual.getName()).contains("Test collection");
+ files.forEach(f -> assertThat(actual.getManifestText()).contains(f.length() + Characters.COLON + f.getName().replace(" ", Characters.SPACE)));
+ }
+
+ @Test
+ public void uploadToExistingCollectionIsPerformedSuccessfully() throws Exception {
+ // given
+ File file = FileTestUtils.generateFile(TEST_FILE, FileTestUtils.ONE_EIGTH_GB / 500);
+ Collection existing = createTestCollection();
+
+ // when
+ Collection actual = FACADE.uploadToExistingCollection(Collections.singletonList(file), collectionUuid);
+
+ // then
+ assertEquals(collectionUuid, actual.getUuid());
+ assertThat(actual.getManifestText()).contains(file.length() + Characters.COLON + file.getName());
+ }
+
+ @Test
+ public void uploadWithExternalConfigProviderWorksProperly() throws Exception {
+ //given
+ ArvadosFacade facade = new ArvadosFacade(buildExternalConfig());
+ File file = FileTestUtils.generateFile(TEST_FILE, FileTestUtils.ONE_FOURTH_GB / 200);
+
+ //when
+ Collection actual = facade.upload(Collections.singletonList(file), COLLECTION_NAME, PROJECT_UUID);
+ collectionUuid = actual.getUuid();
+
+ //then
+ assertThat(actual.getName()).contains("Test collection");
+ assertThat(actual.getManifestText()).contains(file.length() + Characters.COLON + file.getName());
+ }
+
+ @Test
+ public void creationOfEmptyCollectionPerformedSuccesfully() {
+ // given
+ String collectionName = "Empty collection " + UUID.randomUUID().toString();
+
+ // when
+ Collection actual = FACADE.createEmptyCollection(collectionName, PROJECT_UUID);
+ collectionUuid = actual.getUuid();
+
+ // then
+ assertEquals(collectionName, actual.getName());
+ assertEquals(PROJECT_UUID, actual.getOwnerUuid());
+ }
+
+ @Test
+ public void fileTokensAreListedFromCollection() throws Exception {
+ //given
+ List<File> files = uploadTestFiles();
+
+ //when
+ List<FileToken> actual = FACADE.listFileInfoFromCollection(collectionUuid);
+
+ //then
+ assertEquals(files.size(), actual.size());
+ for (int i = 0; i < files.size(); i++) {
+ assertEquals(files.get(i).length(), actual.get(i).getFileSize());
+ }
+ }
+
+ @Test
+ public void downloadOfFilesPerformedSuccessfully() throws Exception {
+ //given
+ List<File> files = uploadTestFiles();
+ File destination = new File(FILE_DOWNLOAD_TEST_DIR + Characters.SLASH + collectionUuid);
+
+ //when
+ List<File> actual = FACADE.downloadCollectionFiles(collectionUuid, FILE_DOWNLOAD_TEST_DIR, false);
+
+ //then
+ assertEquals(files.size(), actual.size());
+ assertTrue(destination.exists());
+ assertThat(actual).allMatch(File::exists);
+ for (int i = 0; i < files.size(); i++) {
+ assertEquals(files.get(i).length(), actual.get(i).length());
+ }
+ }
+
+ @Test
+ public void downloadOfFilesPerformedSuccessfullyUsingKeepWeb() throws Exception {
+ //given
+ List<File> files = uploadTestFiles();
+ File destination = new File(FILE_DOWNLOAD_TEST_DIR + Characters.SLASH + collectionUuid);
+
+ //when
+ List<File> actual = FACADE.downloadCollectionFiles(collectionUuid, FILE_DOWNLOAD_TEST_DIR, true);
+
+ //then
+ assertEquals(files.size(), actual.size());
+ assertTrue(destination.exists());
+ assertThat(actual).allMatch(File::exists);
+ for (int i = 0; i < files.size(); i++) {
+ assertEquals(files.get(i).length(), actual.get(i).length());
+ }
+ }
+
+ @Test
+ public void singleFileIsDownloadedSuccessfullyUsingKeepWeb() throws Exception {
+ //given
+ File file = uploadSingleTestFile(false);
+
+ //when
+ File actual = FACADE.downloadFile(file.getName(), collectionUuid, FILE_DOWNLOAD_TEST_DIR);
+
+ //then
+ assertThat(actual).exists();
+ assertThat(actual.length()).isEqualTo(file.length());
+ }
+
+ @Test
+ public void downloadOfOneFileSplittedToMultipleLocatorsPerformedSuccesfully() throws Exception {
+ //given
+ File file = uploadSingleTestFile(true);
+
+ List<File> actual = FACADE.downloadCollectionFiles(collectionUuid, FILE_DOWNLOAD_TEST_DIR, false);
+
+ Assert.assertEquals(1, actual.size());
+ assertThat(actual.get(0).length()).isEqualTo(file.length());
+ }
+
+ @Test
+ public void downloadWithExternalConfigProviderWorksProperly() throws Exception {
+ //given
+ ArvadosFacade facade = new ArvadosFacade(buildExternalConfig());
+ List<File> files = uploadTestFiles();
+ //when
+ List<File> actual = facade.downloadCollectionFiles(collectionUuid, FILE_DOWNLOAD_TEST_DIR, false);
+
+ //then
+ assertEquals(files.size(), actual.size());
+ assertThat(actual).allMatch(File::exists);
+ for (int i = 0; i < files.size(); i++) {
+ assertEquals(files.get(i).length(), actual.get(i).length());
+ }
+ }
+
+ private ExternalConfigProvider buildExternalConfig() {
+ return ExternalConfigProvider
+ .builder()
+ .apiHostInsecure(CONFIG.isApiHostInsecure())
+ .keepWebHost(CONFIG.getKeepWebHost())
+ .keepWebPort(CONFIG.getKeepWebPort())
+ .apiHost(CONFIG.getApiHost())
+ .apiPort(CONFIG.getApiPort())
+ .apiToken(CONFIG.getApiToken())
+ .apiProtocol(CONFIG.getApiProtocol())
+ .fileSplitSize(CONFIG.getFileSplitSize())
+ .fileSplitDirectory(CONFIG.getFileSplitDirectory())
+ .numberOfCopies(CONFIG.getNumberOfCopies())
+ .numberOfRetries(CONFIG.getNumberOfRetries())
+ .build();
+ }
+
+ private Collection createTestCollection() {
+ Collection collection = FACADE.createEmptyCollection(COLLECTION_NAME, PROJECT_UUID);
+ collectionUuid = collection.getUuid();
+ return collection;
+ }
+
+ private List<File> uploadTestFiles() throws Exception{
+ createTestCollection();
+ List<File> files = FileTestUtils.generatePredefinedFiles();
+ FACADE.uploadToExistingCollection(files, collectionUuid);
+ return files;
+ }
+
+ private File uploadSingleTestFile(boolean bigFile) throws Exception{
+ createTestCollection();
+ Long fileSize = bigFile ? FileUtils.ONE_MB * 70 : FileTestUtils.ONE_EIGTH_GB / 100;
+ File file = FileTestUtils.generateFile(TEST_FILE, fileSize);
+ FACADE.uploadToExistingCollection(Collections.singletonList(file), collectionUuid);
+ return file;
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ FileTestUtils.cleanDirectory(FILE_SPLIT_TEST_DIR);
+ FileTestUtils.cleanDirectory(FILE_DOWNLOAD_TEST_DIR);
+
+ if(collectionUuid != null)
+ FACADE.deleteCollection(collectionUuid);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.facade;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
+import okhttp3.mockwebserver.MockResponse;
+import okio.Buffer;
+import org.apache.commons.io.FileUtils;
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.api.model.KeepService;
+import org.arvados.client.api.model.KeepServiceList;
+import org.arvados.client.common.Characters;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.arvados.client.test.utils.FileTestUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.Ignore;
+
+import java.io.File;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static org.arvados.client.test.utils.ApiClientTestUtils.getResponse;
+import static org.arvados.client.test.utils.FileTestUtils.*;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+public class ArvadosFacadeTest extends ArvadosClientMockedWebServerTest {
+
+ ArvadosFacade facade = new ArvadosFacade(CONFIG);
+
+ @Before
+ public void setUp() throws Exception {
+ FileTestUtils.createDirectory(FILE_SPLIT_TEST_DIR);
+ FileTestUtils.createDirectory(FILE_DOWNLOAD_TEST_DIR);
+ }
+
+ @Test
+ @Ignore("Failing test #15041")
+ public void uploadIsPerformedSuccessfullyUsingDiskOnlyKeepServices() throws Exception {
+
+ // given
+ String keepServicesAccessible = setMockedServerPortToKeepServices("keep-services-accessible-disk-only");
+ server.enqueue(new MockResponse().setBody(keepServicesAccessible));
+
+ String blockLocator = "7df44272090cee6c0732382bba415ee9";
+ String signedBlockLocator = blockLocator + "+70+A189a93acda6e1fba18a9dffd42b6591cbd36d55d@5a1c17b6";
+ for (int i = 0; i < 8; i++) {
+ server.enqueue(new MockResponse().setBody(signedBlockLocator));
+ }
+ server.enqueue(getResponse("users-get"));
+ server.enqueue(getResponse("collections-create-manifest"));
+
+ FileTestUtils.generateFile(TEST_FILE, FileTestUtils.ONE_FOURTH_GB);
+
+ // when
+ Collection actual = facade.upload(Arrays.asList(new File(TEST_FILE)), "Super Collection", null);
+
+ // then
+ assertThat(actual.getName()).contains("Super Collection");
+ }
+
+ @Test
+ public void uploadIsPerformedSuccessfully() throws Exception {
+
+ // given
+ String keepServicesAccessible = setMockedServerPortToKeepServices("keep-services-accessible");
+ server.enqueue(new MockResponse().setBody(keepServicesAccessible));
+
+ String blockLocator = "7df44272090cee6c0732382bba415ee9";
+ String signedBlockLocator = blockLocator + "+70+A189a93acda6e1fba18a9dffd42b6591cbd36d55d@5a1c17b6";
+ for (int i = 0; i < 4; i++) {
+ server.enqueue(new MockResponse().setBody(signedBlockLocator));
+ }
+ server.enqueue(getResponse("users-get"));
+ server.enqueue(getResponse("collections-create-manifest"));
+
+ FileTestUtils.generateFile(TEST_FILE, FileTestUtils.ONE_FOURTH_GB);
+
+ // when
+ Collection actual = facade.upload(Arrays.asList(new File(TEST_FILE)), "Super Collection", null);
+
+ // then
+ assertThat(actual.getName()).contains("Super Collection");
+ }
+
+ @Test
+ public void downloadOfWholeCollectionIsPerformedSuccessfully() throws Exception {
+
+ //given
+ String collectionUuid = "ardev-4zz18-jk5vo4uo9u5vj52";
+ server.enqueue(getResponse("collections-download-file"));
+
+ String keepServicesAccessible = setMockedServerPortToKeepServices("keep-services-accessible");
+ server.enqueue(new MockResponse().setBody(keepServicesAccessible));
+ File collectionDestination = new File(FILE_DOWNLOAD_TEST_DIR + Characters.SLASH + collectionUuid);
+
+ List<File> files = generatePredefinedFiles();
+ List<byte[]> fileData = new ArrayList<>();
+ for (File f : files) {
+ fileData.add(Files.readAllBytes(f.toPath()));
+ }
+ byte[] filesDataChunk = fileData.stream().reduce(new byte[0], this::addAll);
+
+ server.enqueue(new MockResponse().setBody(new Buffer().write(filesDataChunk)));
+
+ //when
+ List<File> downloadedFiles = facade.downloadCollectionFiles(collectionUuid, FILE_DOWNLOAD_TEST_DIR, false);
+
+ //then
+ assertEquals(3, downloadedFiles.size());
+ assertTrue(collectionDestination.exists());
+ assertThat(downloadedFiles).allMatch(File::exists);
+ assertEquals(files.stream().map(File::getName).collect(Collectors.toList()), downloadedFiles.stream().map(File::getName).collect(Collectors.toList()));
+ assertEquals(files.stream().map(File::length).collect(Collectors.toList()), downloadedFiles.stream().map(File::length).collect(Collectors.toList()));
+ }
+
+ @Test
+ public void downloadOfWholeCollectionUsingKeepWebPerformedSuccessfully() throws Exception {
+
+ //given
+ String collectionUuid = "ardev-4zz18-jk5vo4uo9u5vj52";
+ server.enqueue(getResponse("collections-download-file"));
+
+ List<File> files = generatePredefinedFiles();
+ for (File f : files) {
+ server.enqueue(new MockResponse().setBody(new Buffer().write(FileUtils.readFileToByteArray(f))));
+ }
+
+ //when
+ List<File> downloadedFiles = facade.downloadCollectionFiles(collectionUuid, FILE_DOWNLOAD_TEST_DIR, true);
+
+ //then
+ assertEquals(3, downloadedFiles.size());
+ assertThat(downloadedFiles).allMatch(File::exists);
+ assertEquals(files.stream().map(File::getName).collect(Collectors.toList()), downloadedFiles.stream().map(File::getName).collect(Collectors.toList()));
+ assertTrue(downloadedFiles.stream().map(File::length).collect(Collectors.toList()).containsAll(files.stream().map(File::length).collect(Collectors.toList())));
+ }
+
+ @Test
+ public void downloadOfSingleFilePerformedSuccessfully() throws Exception {
+
+ //given
+ String collectionUuid = "ardev-4zz18-jk5vo4uo9u5vj52";
+ server.enqueue(getResponse("collections-download-file"));
+
+ File file = generatePredefinedFiles().get(0);
+ byte[] fileData = FileUtils.readFileToByteArray(file);
+ server.enqueue(new MockResponse().setBody(new Buffer().write(fileData)));
+
+ //when
+ File downloadedFile = facade.downloadFile(file.getName(), collectionUuid, FILE_DOWNLOAD_TEST_DIR);
+
+ //then
+ assertTrue(downloadedFile.exists());
+ assertEquals(file.getName(), downloadedFile.getName());
+ assertEquals(file.length(), downloadedFile.length());
+ }
+
+ private String setMockedServerPortToKeepServices(String jsonPath) throws Exception {
+
+ ObjectMapper mapper = new ObjectMapper().findAndRegisterModules();
+ String filePath = String.format("src/test/resources/org/arvados/client/api/client/%s.json", jsonPath);
+ File jsonFile = new File(filePath);
+ String json = FileUtils.readFileToString(jsonFile, Charset.defaultCharset());
+ KeepServiceList keepServiceList = mapper.readValue(json, KeepServiceList.class);
+ List<KeepService> items = keepServiceList.getItems();
+ for (KeepService keepService : items) {
+ keepService.setServicePort(server.getPort());
+ }
+ ObjectWriter writer = mapper.writer().withDefaultPrettyPrinter();
+ return writer.writeValueAsString(keepServiceList);
+ }
+
+ //Method to copy multiple byte[] arrays into one byte[] array
+ private byte[] addAll(byte[] array1, byte[] array2) {
+ byte[] joinedArray = new byte[array1.length + array2.length];
+ System.arraycopy(array1, 0, joinedArray, 0, array1.length);
+ System.arraycopy(array2, 0, joinedArray, array1.length, array2.length);
+ return joinedArray;
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ FileTestUtils.cleanDirectory(FILE_SPLIT_TEST_DIR);
+ FileTestUtils.cleanDirectory(FILE_DOWNLOAD_TEST_DIR);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.junit.categories;
+
+public interface IntegrationTests {}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+import org.arvados.client.common.Characters;
+import org.junit.Assert;
+import org.junit.Test;
+
+public class FileTokenTest {
+
+ public static final String FILE_TOKEN_INFO = "0:1024:test-file1";
+ public static final int FILE_POSITION = 0;
+ public static final int FILE_LENGTH = 1024;
+ public static final String FILE_NAME = "test-file1";
+ public static final String FILE_PATH = "c" + Characters.SLASH;
+
+ private static FileToken fileToken = new FileToken(FILE_TOKEN_INFO);
+ private static FileToken fileTokenWithPath = new FileToken(FILE_TOKEN_INFO, FILE_PATH);
+
+ @Test
+ public void tokenInfoIsDividedCorrectly(){
+ Assert.assertEquals(FILE_NAME, fileToken.getFileName());
+ Assert.assertEquals(FILE_POSITION, fileToken.getFilePosition());
+ Assert.assertEquals(FILE_LENGTH, fileToken.getFileSize());
+ }
+
+ @Test
+ public void toStringReturnsOriginalFileTokenInfo(){
+ Assert.assertEquals(FILE_TOKEN_INFO, fileToken.toString());
+ }
+
+ @Test
+ public void fullPathIsReturnedProperly(){
+ Assert.assertEquals(FILE_NAME, fileToken.getFullPath());
+ Assert.assertEquals(FILE_PATH + FILE_NAME, fileTokenWithPath.getFullPath());
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+import org.arvados.client.exception.ArvadosClientException;
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.util.List;
+
+import static junit.framework.TestCase.fail;
+
+public class ManifestDecoderTest {
+
+ private ManifestDecoder manifestDecoder = new ManifestDecoder();
+
+ private static final String ONE_LINE_MANIFEST_TEXT = ". " +
+ "eff999f3b5158331eb44a9a93e3b36e1+67108864+Aad3839bea88bce22cbfe71cf4943de7dab3ea52a@5826180f " +
+ "db141bfd11f7da60dce9e5ee85a988b8+34038725+Ae8f48913fed782cbe463e0499ab37697ee06a2f8@5826180f " +
+ "0:101147589:rna.SRR948778.bam" +
+ "\\n";
+
+ private static final String MULTIPLE_LINES_MANIFEST_TEXT = ". " +
+ "930625b054ce894ac40596c3f5a0d947+33 " +
+ "0:0:a 0:0:b 0:33:output.txt\n" +
+ "./c d41d8cd98f00b204e9800998ecf8427e+0 0:0:d";
+
+ private static final String MANIFEST_TEXT_WITH_INVALID_FIRST_PATH_COMPONENT = "a" + ONE_LINE_MANIFEST_TEXT;
+
+
+ @Test
+ public void allLocatorsAndFileTokensAreExtractedFromSimpleManifest() {
+
+ List<ManifestStream> actual = manifestDecoder.decode(ONE_LINE_MANIFEST_TEXT);
+
+ // one manifest stream
+ Assert.assertEquals(1, actual.size());
+
+ ManifestStream manifest = actual.get(0);
+ // two locators
+ Assert.assertEquals(2, manifest.getKeepLocators().size());
+ // one file token
+ Assert.assertEquals(1, manifest.getFileTokens().size());
+
+ }
+
+ @Test
+ public void allLocatorsAndFileTokensAreExtractedFromComplexManifest() {
+
+ List<ManifestStream> actual = manifestDecoder.decode(MULTIPLE_LINES_MANIFEST_TEXT);
+
+ // two manifest streams
+ Assert.assertEquals(2, actual.size());
+
+ // first stream - 1 locator and 3 file tokens
+ ManifestStream firstManifestStream = actual.get(0);
+ Assert.assertEquals(1, firstManifestStream.getKeepLocators().size());
+ Assert.assertEquals(3, firstManifestStream.getFileTokens().size());
+
+ // second stream - 1 locator and 1 file token
+ ManifestStream secondManifestStream = actual.get(1);
+ Assert.assertEquals(1, secondManifestStream.getKeepLocators().size());
+ Assert.assertEquals(1, secondManifestStream.getFileTokens().size());
+ }
+
+ @Test
+ public void manifestTextWithInvalidStreamNameThrowsException() {
+
+ try {
+ List<ManifestStream> actual = manifestDecoder.decode(MANIFEST_TEXT_WITH_INVALID_FIRST_PATH_COMPONENT);
+ fail();
+ } catch (ArvadosClientException e) {
+ Assert.assertEquals("Invalid first path component (expecting \".\")", e.getMessage());
+ }
+
+ }
+
+ @Test
+ public void emptyManifestTextThrowsException() {
+ String emptyManifestText = null;
+
+ try {
+ List<ManifestStream> actual = manifestDecoder.decode(emptyManifestText);
+ fail();
+ } catch (ArvadosClientException e) {
+ Assert.assertEquals("Manifest text cannot be empty.", e.getMessage());
+ }
+
+ emptyManifestText = "";
+ try {
+ List<ManifestStream> actual = manifestDecoder.decode(emptyManifestText);
+ fail();
+ } catch (ArvadosClientException e) {
+ Assert.assertEquals("Manifest text cannot be empty.", e.getMessage());
+ }
+
+ }
+
+
+
+
+
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+import org.arvados.client.test.utils.FileTestUtils;
+import org.assertj.core.util.Lists;
+import org.junit.Test;
+import org.junit.Ignore;
+
+import java.io.File;
+import java.util.List;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class ManifestFactoryTest {
+
+ @Test
+ @Ignore("Failing test #15041")
+ public void manifestIsCreatedAsExpected() throws Exception {
+
+ // given
+ List<File> files = FileTestUtils.generatePredefinedFiles();
+ List<String> locators = Lists.newArrayList("a", "b", "c");
+ ManifestFactory factory = ManifestFactory.builder()
+ .files(files)
+ .locators(locators)
+ .build();
+
+ // when
+ String actual = factory.create();
+
+ // then
+ assertThat(actual).isEqualTo(". a b c 0:1024:test-file1 1024:20480:test-file2 21504:1048576:test-file\\0403\n");
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.collection;
+
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.util.List;
+
+public class ManifestStreamTest {
+
+ private ManifestDecoder manifestDecoder = new ManifestDecoder();
+
+ @Test
+ public void toStringReturnsProperlyConnectedManifestStream() throws Exception{
+ String encodedManifest = ". eff999f3b5158331eb44a9a93e3b36e1+67108864 db141bfd11f7da60dce9e5ee85a988b8+34038725 0:101147589:rna.SRR948778.bam\\n\"";
+ List<ManifestStream> manifestStreams = manifestDecoder.decode(encodedManifest);
+ Assert.assertEquals(encodedManifest, manifestStreams.get(0).toString());
+
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.arvados.client.api.client.CollectionsApiClient;
+import org.arvados.client.api.client.KeepWebApiClient;
+import org.arvados.client.api.model.Collection;
+import org.arvados.client.common.Characters;
+import org.arvados.client.logic.collection.FileToken;
+import org.arvados.client.logic.collection.ManifestDecoder;
+import org.arvados.client.logic.collection.ManifestStream;
+import org.arvados.client.test.utils.FileTestUtils;
+import org.arvados.client.utils.FileMerge;
+import org.apache.commons.io.FileUtils;
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.UUID;
+
+import static org.arvados.client.test.utils.FileTestUtils.*;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.Mockito.when;
+
+@RunWith(MockitoJUnitRunner.class)
+public class FileDownloaderTest {
+
+ static final ObjectMapper MAPPER = new ObjectMapper().findAndRegisterModules();
+ private Collection collectionToDownload;
+ private ManifestStream manifestStream;
+
+ @Mock
+ private CollectionsApiClient collectionsApiClient;
+ @Mock
+ private KeepClient keepClient;
+ @Mock
+ private KeepWebApiClient keepWebApiClient;
+ @Mock
+ private ManifestDecoder manifestDecoder;
+ @InjectMocks
+ private FileDownloader fileDownloader;
+
+ @Before
+ public void setUp() throws Exception {
+ FileTestUtils.createDirectory(FILE_SPLIT_TEST_DIR);
+ FileTestUtils.createDirectory(FILE_DOWNLOAD_TEST_DIR);
+
+ collectionToDownload = prepareCollection();
+ manifestStream = prepareManifestStream();
+ }
+
+ @Test
+ public void downloadingAllFilesFromCollectionWorksProperly() throws Exception {
+ // given
+ List<File> files = generatePredefinedFiles();
+ byte[] dataChunk = prepareDataChunk(files);
+
+ //having
+ when(collectionsApiClient.get(collectionToDownload.getUuid())).thenReturn(collectionToDownload);
+ when(manifestDecoder.decode(collectionToDownload.getManifestText())).thenReturn(Arrays.asList(manifestStream));
+ when(keepClient.getDataChunk(manifestStream.getKeepLocators().get(0))).thenReturn(dataChunk);
+
+ //when
+ List<File> downloadedFiles = fileDownloader.downloadFilesFromCollection(collectionToDownload.getUuid(), FILE_DOWNLOAD_TEST_DIR);
+
+ //then
+ Assert.assertEquals(3, downloadedFiles.size()); // 3 files downloaded
+
+ File collectionDir = new File(FILE_DOWNLOAD_TEST_DIR + Characters.SLASH + collectionToDownload.getUuid());
+ Assert.assertTrue(collectionDir.exists()); // collection directory created
+
+ // 3 files correctly saved
+ assertThat(downloadedFiles).allMatch(File::exists);
+
+ for(int i = 0; i < downloadedFiles.size(); i ++) {
+ File downloaded = new File(collectionDir + Characters.SLASH + files.get(i).getName());
+ Assert.assertArrayEquals(FileUtils.readFileToByteArray(downloaded), FileUtils.readFileToByteArray(files.get(i)));
+ }
+ }
+
+ @Test
+ public void downloadingSingleFileFromKeepWebWorksCorrectly() throws Exception{
+ //given
+ File file = generatePredefinedFiles().get(0);
+
+ //having
+ when(collectionsApiClient.get(collectionToDownload.getUuid())).thenReturn(collectionToDownload);
+ when(manifestDecoder.decode(collectionToDownload.getManifestText())).thenReturn(Arrays.asList(manifestStream));
+ when(keepWebApiClient.download(collectionToDownload.getUuid(), file.getName())).thenReturn(FileUtils.readFileToByteArray(file));
+
+ //when
+ File downloadedFile = fileDownloader.downloadSingleFileUsingKeepWeb(file.getName(), collectionToDownload.getUuid(), FILE_DOWNLOAD_TEST_DIR);
+
+ //then
+ Assert.assertTrue(downloadedFile.exists());
+ Assert.assertEquals(file.getName(), downloadedFile.getName());
+ Assert.assertArrayEquals(FileUtils.readFileToByteArray(downloadedFile), FileUtils.readFileToByteArray(file));
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ FileTestUtils.cleanDirectory(FILE_SPLIT_TEST_DIR);
+ FileTestUtils.cleanDirectory(FILE_DOWNLOAD_TEST_DIR);
+ }
+
+ private Collection prepareCollection() throws IOException {
+ // collection that will be returned by mocked collectionsApiClient
+ String filePath = "src/test/resources/org/arvados/client/api/client/collections-download-file.json";
+ File jsonFile = new File(filePath);
+ return MAPPER.readValue(jsonFile, Collection.class);
+ }
+
+ private ManifestStream prepareManifestStream() throws Exception {
+ // manifestStream that will be returned by mocked manifestDecoder
+ List<FileToken> fileTokens = new ArrayList<>();
+ fileTokens.add(new FileToken("0:1024:test-file1"));
+ fileTokens.add(new FileToken("1024:20480:test-file2"));
+ fileTokens.add(new FileToken("21504:1048576:test-file\\0403"));
+
+ KeepLocator keepLocator = new KeepLocator("163679d58edaadc28db769011728a72c+1070080+A3acf8c1fe582c265d2077702e4a7d74fcc03aba8@5aa4fdeb");
+ return new ManifestStream(".", Arrays.asList(keepLocator), fileTokens);
+ }
+
+ private byte[] prepareDataChunk(List<File> files) throws IOException {
+ File combinedFile = new File(FILE_SPLIT_TEST_DIR + Characters.SLASH + UUID.randomUUID());
+ FileMerge.merge(files, combinedFile);
+ return FileUtils.readFileToByteArray(combinedFile);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep;
+
+import okhttp3.mockwebserver.MockResponse;
+import okio.Buffer;
+import org.apache.commons.io.FileUtils;
+import org.arvados.client.config.FileConfigProvider;
+import org.arvados.client.config.ConfigProvider;
+import org.arvados.client.exception.ArvadosClientException;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.junit.Assert;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.io.File;
+
+import static junit.framework.TestCase.fail;
+import static org.arvados.client.test.utils.ApiClientTestUtils.getResponse;
+import static org.assertj.core.api.Assertions.assertThat;
+
+@RunWith(MockitoJUnitRunner.class)
+public class KeepClientTest extends ArvadosClientMockedWebServerTest {
+
+ private ConfigProvider configProvider = new FileConfigProvider();
+ private static final String TEST_FILE_PATH ="src/test/resources/org/arvados/client/api/client/keep-client-test-file.txt";
+
+ @InjectMocks
+ private KeepClient keepClient = new KeepClient(configProvider);
+
+ @Mock
+ private KeepLocator keepLocator;
+
+ @Test
+ public void uploadedFile() throws Exception {
+ // given
+ server.enqueue(getResponse("keep-services-accessible"));
+ server.enqueue(new MockResponse().setBody("0887c78c7d6c1a60ac0b3709a4302ee4"));
+
+ // when
+ String actual = keepClient.put(new File(TEST_FILE_PATH), 1, 0);
+
+ // then
+ assertThat(actual).isEqualTo("0887c78c7d6c1a60ac0b3709a4302ee4");
+ }
+
+ @Test
+ public void fileIsDownloaded() throws Exception {
+ //given
+ File data = new File(TEST_FILE_PATH);
+ byte[] fileBytes = FileUtils.readFileToByteArray(data);
+
+ // when
+ server.enqueue(getResponse("keep-services-accessible"));
+ server.enqueue(new MockResponse().setBody(new Buffer().write(fileBytes)));
+
+ byte[] actual = keepClient.getDataChunk(keepLocator);
+
+ Assert.assertArrayEquals(fileBytes, actual);
+ }
+
+ @Test
+ public void fileIsDownloadedWhenFirstServerDoesNotRespond() throws Exception {
+ // given
+ File data = new File(TEST_FILE_PATH);
+ byte[] fileBytes = FileUtils.readFileToByteArray(data);
+ server.enqueue(getResponse("keep-services-accessible")); // two servers accessible
+ server.enqueue(new MockResponse().setResponseCode(404)); // first one not responding
+ server.enqueue(new MockResponse().setBody(new Buffer().write(fileBytes))); // second one responding
+
+ //when
+ byte[] actual = keepClient.getDataChunk(keepLocator);
+
+ //then
+ Assert.assertArrayEquals(fileBytes, actual);
+ }
+
+ @Test
+ public void exceptionIsThrownWhenNoServerResponds() throws Exception {
+ //given
+ File data = new File(TEST_FILE_PATH);
+ server.enqueue(getResponse("keep-services-accessible")); // two servers accessible
+ server.enqueue(new MockResponse().setResponseCode(404)); // first one not responding
+ server.enqueue(new MockResponse().setResponseCode(404)); // second one not responding
+
+ try {
+ //when
+ keepClient.getDataChunk(keepLocator);
+ fail();
+ } catch (ArvadosClientException e) {
+ //then
+ Assert.assertEquals("No server responding. Unable to download data chunk.", e.getMessage());
+ }
+ }
+
+ @Test
+ public void exceptionIsThrownWhenThereAreNoServersAccessible() throws Exception {
+ //given
+ server.enqueue(getResponse("keep-services-not-accessible")); // no servers accessible
+
+ try {
+ //when
+ keepClient.getDataChunk(keepLocator);
+ fail();
+ } catch (ArvadosClientException e) {
+ //then
+ Assert.assertEquals("No gateway services available!", e.getMessage());
+ }
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.logic.keep;
+
+import org.junit.Test;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class KeepLocatorTest {
+
+ private KeepLocator locator;
+
+ @Test
+ public void md5sumIsExtracted() throws Exception {
+
+ // given
+ locator = new KeepLocator("7df44272090cee6c0732382bba415ee9+70");
+
+ // when
+ String actual = locator.getMd5sum();
+
+ // then
+ assertThat(actual).isEqualTo("7df44272090cee6c0732382bba415ee9");
+ }
+
+ @Test
+ public void locatorIsStrippedWithMd5sumAndSize() throws Exception {
+
+ // given
+ locator = new KeepLocator("7df44272090cee6c0732382bba415ee9+70");
+
+ // when
+ String actual = locator.stripped();
+
+ // then
+ assertThat(actual).isEqualTo("7df44272090cee6c0732382bba415ee9+70");
+ }
+
+
+ @Test
+ public void locatorToStringProperlyShowing() throws Exception {
+
+ // given
+ locator = new KeepLocator("7df44272090cee6c0732382bba415ee9+70+Ae8f48913fed782cbe463e0499ab37697ee06a2f8@5826180f");
+
+ // when
+ String actual = locator.toString();
+
+ // then
+ assertThat(actual).isEqualTo("7df44272090cee6c0732382bba415ee9+70+Ae8f48913fed782cbe463e0499ab37697ee06a2f8@5826180f");
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.test.utils;
+
+import org.arvados.client.config.FileConfigProvider;
+import okhttp3.mockwebserver.MockResponse;
+import okhttp3.mockwebserver.RecordedRequest;
+import org.apache.commons.io.FileUtils;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.Charset;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public final class ApiClientTestUtils {
+
+ static final String BASE_URL = "/arvados/v1/";
+
+ private ApiClientTestUtils() {}
+
+ public static MockResponse getResponse(String filename) throws IOException {
+ String filePath = String.format("src/test/resources/org/arvados/client/api/client/%s.json", filename);
+ File jsonFile = new File(filePath);
+ String json = FileUtils.readFileToString(jsonFile, Charset.defaultCharset());
+ return new MockResponse().setBody(json);
+ }
+
+ public static void assertAuthorizationHeader(RecordedRequest request) {
+ assertThat(request.getHeader("authorization")).isEqualTo("OAuth2 " + new FileConfigProvider().getApiToken());
+ }
+
+ public static void assertRequestPath(RecordedRequest request, String subPath) {
+ assertThat(request.getPath()).isEqualTo(BASE_URL + subPath);
+ }
+
+ public static void assertRequestMethod(RecordedRequest request, RequestMethod requestMethod) {
+ assertThat(request.getMethod()).isEqualTo(requestMethod.name());
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.test.utils;
+
+import org.arvados.client.config.FileConfigProvider;
+import org.arvados.client.facade.ArvadosFacade;
+import org.junit.BeforeClass;
+
+import static org.junit.Assert.assertTrue;
+
+public class ArvadosClientIntegrationTest {
+
+ protected static final FileConfigProvider CONFIG = new FileConfigProvider("integration-tests-application.conf");
+ protected static final ArvadosFacade FACADE = new ArvadosFacade(CONFIG);
+ protected static final String PROJECT_UUID = CONFIG.getIntegrationTestProjectUuid();
+
+ @BeforeClass
+ public static void validateConfiguration(){
+ String msg = " info must be provided in configuration";
+ CONFIG.getConfig().entrySet()
+ .forEach(e -> assertTrue("Parameter " + e.getKey() + msg, !e.getValue().render().equals("\"\"")));
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.test.utils;
+
+import okhttp3.mockwebserver.MockWebServer;
+import org.junit.After;
+import org.junit.Before;
+
+public class ArvadosClientMockedWebServerTest extends ArvadosClientUnitTest {
+ private static final int PORT = CONFIG.getApiPort();
+ protected MockWebServer server = new MockWebServer();
+
+ @Before
+ public void setUpServer() throws Exception {
+ server.start(PORT);
+ }
+
+ @After
+ public void tearDownServer() throws Exception {
+ server.shutdown();
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.test.utils;
+
+import org.arvados.client.config.FileConfigProvider;
+import org.junit.BeforeClass;
+
+import static org.junit.Assert.assertTrue;
+
+public class ArvadosClientUnitTest {
+
+ protected static final FileConfigProvider CONFIG = new FileConfigProvider("application.conf");
+
+ @BeforeClass
+ public static void validateConfiguration(){
+ String msg = " info must be provided in configuration";
+ CONFIG.getConfig().entrySet().forEach(e -> assertTrue("Parameter " + e.getKey() + msg, !e.getValue().render().equals("\"\"")));
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.test.utils;
+
+import org.apache.commons.io.FileUtils;
+import org.assertj.core.util.Lists;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.RandomAccessFile;
+import java.util.List;
+
+public class FileTestUtils {
+
+ public static final String FILE_SPLIT_TEST_DIR = "/tmp/file-split";
+ public static final String FILE_DOWNLOAD_TEST_DIR = "/tmp/arvados-downloaded";
+ public static final String TEST_FILE = FILE_SPLIT_TEST_DIR + "/test-file";
+ public static long ONE_FOURTH_GB = FileUtils.ONE_GB / 4;
+ public static long ONE_EIGTH_GB = FileUtils.ONE_GB / 8;
+ public static long HALF_GB = FileUtils.ONE_GB / 2;
+ public static int FILE_SPLIT_SIZE = 64;
+
+ public static void createDirectory(String path) throws Exception {
+ new File(path).mkdirs();
+ }
+
+ public static void cleanDirectory(String directory) throws Exception {
+ FileUtils.cleanDirectory(new File(directory));
+ }
+
+ public static File generateFile(String path, long length) throws IOException {
+ RandomAccessFile testFile = new RandomAccessFile(path, "rwd");
+ testFile.setLength(length);
+ testFile.close();
+ return new File(path);
+ }
+
+ public static List<File> generatePredefinedFiles() throws IOException {
+ return Lists.newArrayList(
+ generateFile(TEST_FILE + 1, FileUtils.ONE_KB),
+ generateFile(TEST_FILE + 2, FileUtils.ONE_KB * 20),
+ generateFile(TEST_FILE + " " + 3, FileUtils.ONE_MB)
+ );
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.test.utils;
+
+public enum RequestMethod {
+
+ GET, POST, PUT, DELETE
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.utils;
+
+import org.arvados.client.test.utils.FileTestUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.List;
+
+import static org.arvados.client.test.utils.FileTestUtils.*;
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class FileMergeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ FileTestUtils.createDirectory(FILE_SPLIT_TEST_DIR);
+ }
+
+ @Test
+ public void fileChunksAreMergedIntoOneFile() throws Exception {
+
+ // given
+ FileTestUtils.generateFile(TEST_FILE, FileTestUtils.ONE_EIGTH_GB);
+
+ List<File> files = FileSplit.split(new File(TEST_FILE), new File(FILE_SPLIT_TEST_DIR), FILE_SPLIT_SIZE);
+ File targetFile = new File(TEST_FILE);
+
+ // when
+ FileMerge.merge(files, targetFile);
+
+ // then
+ assertThat(targetFile.length()).isEqualTo(FileTestUtils.ONE_EIGTH_GB);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ FileTestUtils.cleanDirectory(FILE_SPLIT_TEST_DIR);
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.utils;
+
+import org.arvados.client.test.utils.FileTestUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.List;
+
+import static org.arvados.client.test.utils.FileTestUtils.*;
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class FileSplitTest {
+
+ @Before
+ public void setUp() throws Exception {
+ FileTestUtils.createDirectory(FILE_SPLIT_TEST_DIR);
+ }
+
+ @Test
+ public void fileIsDividedIntoSmallerChunks() throws Exception {
+
+ // given
+ int expectedSize = 2;
+ int expectedFileSizeInBytes = 67108864;
+ FileTestUtils.generateFile(TEST_FILE, FileTestUtils.ONE_EIGTH_GB);
+
+ // when
+ List<File> actual = FileSplit.split(new File(TEST_FILE), new File(FILE_SPLIT_TEST_DIR), FILE_SPLIT_SIZE);
+
+ // then
+ assertThat(actual).hasSize(expectedSize);
+ assertThat(actual).allMatch(a -> a.length() == expectedFileSizeInBytes);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ FileTestUtils.cleanDirectory(FILE_SPLIT_TEST_DIR);
+ }
+}
--- /dev/null
+# configuration for unit tests
+
+arvados {
+ api {
+ port = 9000
+ keepweb-port = 9000
+ token = 1m69yw9m2wanubzyfkb1e9icplqhtr2r969bu9rnzqbqhb7cnb
+ protocol = "http"
+ }
+}
\ No newline at end of file
--- /dev/null
+# Configuration for integration tests
+#
+# Remarks:
+# * For example see integration-tests-application.conf.example
+# * While providing data remove apostrophes ("") from each line
+# * See Arvados documentation for information how to obtain a token:
+# https://doc.arvados.org/user/reference/api-tokens.html
+#
+
+arvados {
+ api {
+ keepweb-host = ""
+ keepweb-port = 443
+ host = ""
+ port = 443
+ token = ""
+ protocol = https
+ host-insecure = false
+ }
+ integration-tests {
+ project-uuid = ""
+ }
+}
--- /dev/null
+# example configuration for integration tests
+
+arvados {
+ api {
+ keepweb-host = collections.ardev.mycompany.com
+ keepweb-port = 443
+ host = api.ardev.mycompany.com
+ port = 443
+ token = mytoken
+ protocol = https
+ host-insecure = false
+ }
+ integration-tests {
+ project-uuid = ardev-j7d0g-aa123f81q6y7skk
+ }
+}
\ No newline at end of file
--- /dev/null
+mock-maker-inline
\ No newline at end of file
--- /dev/null
+{
+ "href": "/collections/112ci-4zz18-12tncxzptzbec1p",
+ "kind": "arvados#collection",
+ "etag": "bqoujj7oybdx0jybwvtsebj7y",
+ "uuid": "112ci-4zz18-12tncxzptzbec1p",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-21T13:38:56.521853000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-21T13:38:56.521853000Z",
+ "name": "Super Collection",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "d41d8cd98f00b204e9800998ecf8427e+0",
+ "manifest_text": ". 7df44272090cee6c0732382bba415ee9+70+Aa5ece4560e3329315165b36c239b8ab79c888f8a@5a1d5708 0:70:README.md\n",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/collections/112ci-4zz18-12tncxzptzbec1p",
+ "kind": "arvados#collection",
+ "etag": "bqoujj7oybdx0jybwvtsebj7y",
+ "uuid": "112ci-4zz18-12tncxzptzbec1p",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-21T13:38:56.521853000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-21T13:38:56.521853000Z",
+ "name": "Super Collection",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "d41d8cd98f00b204e9800998ecf8427e+0",
+ "manifest_text": "",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/collections/ardev-4zz18-jk5vo4uo9u5vj52",
+ "kind": "arvados#collection",
+ "etag": "2vm76dxmzr23u9774iguuxsrg",
+ "uuid": "ardev-4zz18-jk5vo4uo9u5vj52",
+ "owner_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "created_at": "2018-02-19T11:00:00.852389000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2018-02-19T11:00:00.852389000Z",
+ "name": "New Collection (2018-02-19 12:00:00.273)",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "49581091dfad651945c12b08d4735d88+112",
+ "manifest_text": ". 163679d58edaadc28db769011728a72c+1070080+A3acf8c1fe582c265d2077702e4a7d74fcc03aba8@5aa4fdeb 0:1024:test-file1 1024:20480:test-file2 21504:1048576:test-file\\0403\n",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/collections/112ci-4zz18-p51w7z3fpopo6sm",
+ "kind": "arvados#collection",
+ "etag": "52tk5yg024cwhkkcidu3zcmj2",
+ "uuid": "112ci-4zz18-p51w7z3fpopo6sm",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-15T10:36:03.554356000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-15T10:36:03.554356000Z",
+ "name": "Collection With Manifest #2",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "6c4106229b08fe25f48b3a7a8289dd46+143",
+ "manifest_text": ". 66c9daa69630e092e9ce554b7aae8a20+524288+A4a15ffea58f259e09f68d3f7eea29942750a79d0@5a269ff6 435f38dd384b06c248feabee0cabca52+524288+A8a99e8148bd368c49901526098901bb7d7890c3b@5a269ff6 dc5b6c104aab35fff6d70a4dadc28d37+391727+Ab0662d549c422c983fccaad02b4ade7b48a8255b@5a269ff6 0:1440303:lombok.jar\n",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+}
\ No newline at end of file
--- /dev/null
+{
+ "kind": "arvados#collectionList",
+ "etag": "",
+ "self_link": "",
+ "offset": 0,
+ "limit": 100,
+ "items": [
+ {
+ "href": "/collections/112ci-4zz18-x6xfmvz0chnkzgv",
+ "kind": "arvados#collection",
+ "etag": "8xyiwnih5b5vzmj5sa33348a7",
+ "uuid": "112ci-4zz18-x6xfmvz0chnkzgv",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-15T13:06:36.934337000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-15T13:06:36.934337000Z",
+ "name": "Collection With Manifest #3",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "6c4106229b08fe25f48b3a7a8289dd46+143",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-p51w7z3fpopo6sm",
+ "kind": "arvados#collection",
+ "etag": "8cmhep8aixe4p42pxjoct5502",
+ "uuid": "112ci-4zz18-p51w7z3fpopo6sm",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-15T10:36:03.554356000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-15T10:36:03.554356000Z",
+ "name": "Collection With Manifest #2",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "6c4106229b08fe25f48b3a7a8289dd46+143",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-xb6gf2yraln7cwa",
+ "kind": "arvados#collection",
+ "etag": "de2ol2dyvsba3mn46al760cyg",
+ "uuid": "112ci-4zz18-xb6gf2yraln7cwa",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-15T09:32:44.146172000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-15T09:32:44.146172000Z",
+ "name": "New collection",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "d41d8cd98f00b204e9800998ecf8427e+0",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-r5jfktpn3a9o0ap",
+ "kind": "arvados#collection",
+ "etag": "dby68gd0vatvi090cu0axvtq3",
+ "uuid": "112ci-4zz18-r5jfktpn3a9o0ap",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-14T13:00:35.431046000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-14T13:00:35.431046000Z",
+ "name": "Collection With Manifest #1",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "3c59518bf8e1100d420488d822682b4a+53",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-nqxk8xjn6mtskzt",
+ "kind": "arvados#collection",
+ "etag": "2b34uzau862w862a2rv36agv6",
+ "uuid": "112ci-4zz18-nqxk8xjn6mtskzt",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-14T12:59:34.767068000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-14T12:59:34.767068000Z",
+ "name": "Empty Collection #2",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "d41d8cd98f00b204e9800998ecf8427e+0",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-rs9bcf5qnyfjrkm",
+ "kind": "arvados#collection",
+ "etag": "60aywazztwfspnasltufcjxpa",
+ "uuid": "112ci-4zz18-rs9bcf5qnyfjrkm",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-14T12:52:33.124452000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-14T12:52:33.124452000Z",
+ "name": "Empty Collection #1",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "d41d8cd98f00b204e9800998ecf8427e+0",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-af656lee4kv7q2m",
+ "kind": "arvados#collection",
+ "etag": "1jward6snif3tsjzftxh8hvwh",
+ "uuid": "112ci-4zz18-af656lee4kv7q2m",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-14T12:09:05.319319000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-14T12:09:05.319319000Z",
+ "name": "create example",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "d41d8cd98f00b204e9800998ecf8427e+0",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-y2zqix7k9an7nro",
+ "kind": "arvados#collection",
+ "etag": "zs2n4zliu6nb5yk3rw6h5ugw",
+ "uuid": "112ci-4zz18-y2zqix7k9an7nro",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-13T16:59:02.299257000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-13T16:59:02.299257000Z",
+ "name": "Saved at 2017-11-13 16:59:01 UTC by VirtualBox",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "5ba3fc508718fabfa20d24390fe31856+53",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-wq77jfi62u5i4rv",
+ "kind": "arvados#collection",
+ "etag": "eijhemzgy44ofmu0dtrowl604",
+ "uuid": "112ci-4zz18-wq77jfi62u5i4rv",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-13T16:58:10.637548000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-13T16:58:10.637548000Z",
+ "name": "Saved at 2017-11-13 16:58:07 UTC by VirtualBox",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "5ba3fc508718fabfa20d24390fe31856+53",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-unaeckkjgeg7ui0",
+ "kind": "arvados#collection",
+ "etag": "1oq7ye0gfbf3ih6y864w3n683",
+ "uuid": "112ci-4zz18-unaeckkjgeg7ui0",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-10T09:43:07.583862000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-10T09:43:07.583862000Z",
+ "name": "Saved at 2017-11-10 09:43:03 UTC by VirtualBox",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "5ba3fc508718fabfa20d24390fe31856+53",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-5y6atonkxq55lms",
+ "kind": "arvados#collection",
+ "etag": "4qmqlro878yx8q7ikhilo8qwn",
+ "uuid": "112ci-4zz18-5y6atonkxq55lms",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-09T12:46:15.245770000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-09T12:46:15.245770000Z",
+ "name": "Saved at 2017-11-09 12:46:13 UTC by VirtualBox",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "5ba3fc508718fabfa20d24390fe31856+53",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/collections/112ci-4zz18-b3fjqd01pxjvseo",
+ "kind": "arvados#collection",
+ "etag": "91v698hngoz241c38bbmh0ogc",
+ "uuid": "112ci-4zz18-b3fjqd01pxjvseo",
+ "owner_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "created_at": "2017-11-09T11:54:07.259998000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-f4633qdjs6w8zcy",
+ "modified_by_user_uuid": "112ci-tpzed-nd84czdo4iea1mz",
+ "modified_at": "2017-11-09T11:54:07.259998000Z",
+ "name": "Saved at 2017-11-09 11:54:04 UTC by VirtualBox",
+ "description": null,
+ "properties": {},
+ "portable_data_hash": "5ba3fc508718fabfa20d24390fe31856+53",
+ "replication_desired": null,
+ "replication_confirmed": null,
+ "replication_confirmed_at": null,
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
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+ "owner_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "created_at": "2018-04-06T15:29:27.754408000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2018-04-06T15:29:27.754408000Z",
+ "name": "TestProject14",
+ "group_class": "project",
+ "description": null,
+ "writable_by": [
+ "ardev-tpzed-n3kzq4fvoks3uw4",
+ "ardev-tpzed-n3kzq4fvoks3uw4"
+ ],
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/groups/ardev-j7d0g-0jbezvnq8i07l7p",
+ "kind": "arvados#group",
+ "etag": "7dbxhvbcfaogwnvo8k4mtqthk",
+ "uuid": "ardev-j7d0g-0jbezvnq8i07l7p",
+ "owner_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "created_at": "2018-04-05T09:32:46.946417000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2018-04-05T09:32:46.946417000Z",
+ "name": "TestProject15",
+ "group_class": "project",
+ "description": null,
+ "writable_by": [
+ "ardev-tpzed-n3kzq4fvoks3uw4",
+ "ardev-tpzed-n3kzq4fvoks3uw4"
+ ],
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/groups/ardev-j7d0g-72dxer22g6iltqz",
+ "kind": "arvados#group",
+ "etag": "dhfu203rckzdzvx832wm7jv59",
+ "uuid": "ardev-j7d0g-72dxer22g6iltqz",
+ "owner_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "created_at": "2018-03-29T11:27:02.482218000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2018-03-29T13:17:00.045606000Z",
+ "name": "TestProject16",
+ "group_class": "project",
+ "description": null,
+ "writable_by": [
+ "ardev-tpzed-n3kzq4fvoks3uw4",
+ "ardev-tpzed-n3kzq4fvoks3uw4"
+ ],
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/groups/ardev-j7d0g-nebzwquxtq1v3o5",
+ "kind": "arvados#group",
+ "etag": "7l9oxbdf4e1m9ddnujokf7czz",
+ "uuid": "ardev-j7d0g-nebzwquxtq1v3o5",
+ "owner_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "created_at": "2018-03-29T11:11:26.235411000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2018-03-29T11:11:26.235411000Z",
+ "name": "TestProject17",
+ "group_class": "project",
+ "description": null,
+ "writable_by": [
+ "ardev-tpzed-n3kzq4fvoks3uw4",
+ "ardev-tpzed-n3kzq4fvoks3uw4"
+ ],
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/groups/ardev-j7d0g-5589c8dmxevecqh",
+ "kind": "arvados#group",
+ "etag": "83862x2o4453mja2rvypjl5gv",
+ "uuid": "ardev-j7d0g-5589c8dmxevecqh",
+ "owner_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "created_at": "2018-03-29T11:10:58.496482000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2018-03-29T11:10:58.496482000Z",
+ "name": "TestProject18",
+ "group_class": "project",
+ "description": null,
+ "writable_by": [
+ "ardev-tpzed-n3kzq4fvoks3uw4",
+ "ardev-tpzed-n3kzq4fvoks3uw4"
+ ],
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/groups/ardev-j7d0g-bmg3pfqtx3ivczp",
+ "kind": "arvados#group",
+ "etag": "3hw0vk4mbl0ofvia5k6x4dwrx",
+ "uuid": "ardev-j7d0g-bmg3pfqtx3ivczp",
+ "owner_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "created_at": "2018-03-29T11:09:05.984597000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2018-03-29T11:09:05.984597000Z",
+ "name": "TestProject19",
+ "group_class": "project",
+ "description": null,
+ "writable_by": [
+ "ardev-tpzed-n3kzq4fvoks3uw4",
+ "ardev-tpzed-n3kzq4fvoks3uw4"
+ ],
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ },
+ {
+ "href": "/groups/ardev-j7d0g-mfitz2oa4rpycou",
+ "kind": "arvados#group",
+ "etag": "6p9xbxpttj782mpqs537gfvc6",
+ "uuid": "ardev-j7d0g-mfitz2oa4rpycou",
+ "owner_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "created_at": "2018-03-29T11:00:19.809612000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2018-03-29T11:00:19.809612000Z",
+ "name": "TestProject20",
+ "group_class": "project",
+ "description": null,
+ "writable_by": [
+ "ardev-tpzed-n3kzq4fvoks3uw4",
+ "ardev-tpzed-n3kzq4fvoks3uw4"
+ ],
+ "delete_at": null,
+ "trash_at": null,
+ "is_trashed": false
+ }
+ ],
+ "items_available": 20
+}
\ No newline at end of file
--- /dev/null
+Sample text file to test keep client.
\ No newline at end of file
--- /dev/null
+{
+ "kind": "arvados#keepServiceList",
+ "etag": "",
+ "self_link": "",
+ "offset": null,
+ "limit": null,
+ "items": [
+ {
+ "href": "/keep_services/112ci-bi6l4-hv02fg8sbti8ykk",
+ "kind": "arvados#keepService",
+ "etag": "bjzh7og2d9z949lbd38vnnslt",
+ "uuid": "112ci-bi6l4-hv02fg8sbti8ykk",
+ "owner_uuid": "112ci-tpzed-000000000000000",
+ "created_at": "2017-11-03T10:04:48.314229000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-xxy0ipzwti8gnmt",
+ "modified_by_user_uuid": "112ci-tpzed-000000000000000",
+ "modified_at": "2017-11-03T10:04:48.314229000Z",
+ "service_host": "localhost",
+ "service_port": 9000,
+ "service_ssl_flag": false,
+ "service_type": "disk",
+ "read_only": false
+ },
+ {
+ "href": "/keep_services/112ci-bi6l4-f0r03wrqymotwql",
+ "kind": "arvados#keepService",
+ "etag": "7m64l69kko4bytpsykf8cay7t",
+ "uuid": "112ci-bi6l4-f0r03wrqymotwql",
+ "owner_uuid": "112ci-tpzed-000000000000000",
+ "created_at": "2017-11-03T10:04:48.351577000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-xxy0ipzwti8gnmt",
+ "modified_by_user_uuid": "112ci-tpzed-000000000000000",
+ "modified_at": "2017-11-03T10:04:48.351577000Z",
+ "service_host": "localhost",
+ "service_port": 9001,
+ "service_ssl_flag": false,
+ "service_type": "disk",
+ "read_only": false
+ }
+ ],
+ "items_available": 2
+}
\ No newline at end of file
--- /dev/null
+{
+ "kind": "arvados#keepServiceList",
+ "etag": "",
+ "self_link": "",
+ "offset": null,
+ "limit": null,
+ "items": [
+ {
+ "href": "/keep_services/112ci-bi6l4-hv02fg8sbti8ykk",
+ "kind": "arvados#keepService",
+ "etag": "bjzh7og2d9z949lbd38vnnslt",
+ "uuid": "112ci-bi6l4-hv02fg8sbti8ykk",
+ "owner_uuid": "112ci-tpzed-000000000000000",
+ "created_at": "2017-11-03T10:04:48.314229000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-xxy0ipzwti8gnmt",
+ "modified_by_user_uuid": "112ci-tpzed-000000000000000",
+ "modified_at": "2017-11-03T10:04:48.314229000Z",
+ "service_host": "localhost",
+ "service_port": 9000,
+ "service_ssl_flag": false,
+ "service_type": "disk",
+ "read_only": false
+ },
+ {
+ "href": "/keep_services/112ci-bi6l4-f0r03wrqymotwql",
+ "kind": "arvados#keepService",
+ "etag": "7m64l69kko4bytpsykf8cay7t",
+ "uuid": "112ci-bi6l4-f0r03wrqymotwql",
+ "owner_uuid": "112ci-tpzed-000000000000000",
+ "created_at": "2017-11-03T10:04:48.351577000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-xxy0ipzwti8gnmt",
+ "modified_by_user_uuid": "112ci-tpzed-000000000000000",
+ "modified_at": "2017-11-03T10:04:48.351577000Z",
+ "service_host": "localhost",
+ "service_port": 9000,
+ "service_ssl_flag": false,
+ "service_type": "gpfs",
+ "read_only": false
+ }
+ ],
+ "items_available": 2
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/keep_services/112ci-bi6l4-hv02fg8sbti8ykk",
+ "kind": "arvados#keepService",
+ "etag": "bjzh7og2d9z949lbd38vnnslt",
+ "uuid": "112ci-bi6l4-hv02fg8sbti8ykk",
+ "owner_uuid": "112ci-tpzed-000000000000000",
+ "created_at": "2017-11-03T10:04:48.314229000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-xxy0ipzwti8gnmt",
+ "modified_by_user_uuid": "112ci-tpzed-000000000000000",
+ "modified_at": "2017-11-03T10:04:48.314229000Z",
+ "service_host": "10.0.2.15",
+ "service_port": 9000,
+ "service_ssl_flag": false,
+ "service_type": "disk",
+ "read_only": false
+}
\ No newline at end of file
--- /dev/null
+{
+ "kind": "arvados#keepServiceList",
+ "etag": "",
+ "self_link": "",
+ "offset": 0,
+ "limit": 100,
+ "items": [
+ {
+ "href": "/keep_services/112ci-bi6l4-f0r03wrqymotwql",
+ "kind": "arvados#keepService",
+ "etag": "7m64l69kko4bytpsykf8cay7t",
+ "uuid": "112ci-bi6l4-f0r03wrqymotwql",
+ "owner_uuid": "112ci-tpzed-000000000000000",
+ "created_at": "2017-11-03T10:04:48.351577000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-xxy0ipzwti8gnmt",
+ "modified_by_user_uuid": "112ci-tpzed-000000000000000",
+ "modified_at": "2017-11-03T10:04:48.351577000Z",
+ "service_host": "10.0.2.15",
+ "service_port": 9000,
+ "service_ssl_flag": false,
+ "service_type": "disk",
+ "read_only": false
+ },
+ {
+ "href": "/keep_services/112ci-bi6l4-hv02fg8sbti8ykk",
+ "kind": "arvados#keepService",
+ "etag": "bjzh7og2d9z949lbd38vnnslt",
+ "uuid": "112ci-bi6l4-hv02fg8sbti8ykk",
+ "owner_uuid": "112ci-tpzed-000000000000000",
+ "created_at": "2017-11-03T10:04:48.314229000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-xxy0ipzwti8gnmt",
+ "modified_by_user_uuid": "112ci-tpzed-000000000000000",
+ "modified_at": "2017-11-03T10:04:48.314229000Z",
+ "service_host": "10.0.2.15",
+ "service_port": 9001,
+ "service_ssl_flag": false,
+ "service_type": "disk",
+ "read_only": false
+ },
+ {
+ "href": "/keep_services/112ci-bi6l4-ko27cfbsf2ssx2m",
+ "kind": "arvados#keepService",
+ "etag": "4be61qkpt6nzdfff4vj9nkpmj",
+ "uuid": "112ci-bi6l4-ko27cfbsf2ssx2m",
+ "owner_uuid": "112ci-tpzed-000000000000000",
+ "created_at": "2017-11-03T10:04:36.355045000Z",
+ "modified_by_client_uuid": "112ci-ozdt8-xxy0ipzwti8gnmt",
+ "modified_by_user_uuid": "112ci-tpzed-000000000000000",
+ "modified_at": "2017-11-03T10:04:36.355045000Z",
+ "service_host": "10.0.2.15",
+ "service_port": 9002,
+ "service_ssl_flag": false,
+ "service_type": "proxy",
+ "read_only": false
+ }
+ ],
+ "items_available": 3
+}
\ No newline at end of file
--- /dev/null
+{
+ "kind": "arvados#keepServiceList",
+ "etag": "",
+ "self_link": "",
+ "offset": null,
+ "limit": null,
+ "items": [],
+ "items_available": 0
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/users/ardev-tpzed-q6dvn7sby55up1b",
+ "kind": "arvados#user",
+ "etag": "b21emst9eu9u1wdpqcz6la583",
+ "uuid": "ardev-tpzed-q6dvn7sby55up1b",
+ "owner_uuid": "ardev-tpzed-000000000000000",
+ "created_at": "2017-10-30T19:42:43.324740000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-o3km4ug9jhs189j",
+ "modified_at": "2017-10-31T09:01:03.985749000Z",
+ "email": "example@email.com",
+ "username": "johnwayne",
+ "full_name": "John Wayne",
+ "first_name": "John",
+ "last_name": "Wayne",
+ "identity_url": "ardev-tpzed-r09t5ztf5qd3rlj",
+ "is_active": true,
+ "is_admin": null,
+ "is_invited": true,
+ "prefs": {},
+ "writable_by": [
+ "ardev-tpzed-000000000000000",
+ "ardev-tpzed-q6dvn7sby55up1b",
+ "ardev-j7d0g-000000000000000"
+ ]
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/users/ardev-tpzed-q6dvn7sby55up1b",
+ "kind": "arvados#user",
+ "etag": "b21emst9eu9u1wdpqcz6la583",
+ "uuid": "ardev-tpzed-q6dvn7sby55up1b",
+ "owner_uuid": "ardev-tpzed-000000000000000",
+ "created_at": "2017-10-30T19:42:43.324740000Z",
+ "modified_by_client_uuid": "ardev-ozdt8-97tzh5x96spqkay",
+ "modified_by_user_uuid": "ardev-tpzed-o3km4ug9jhs189j",
+ "modified_at": "2017-10-31T09:01:03.985749000Z",
+ "email": "example@email.com",
+ "username": "johnwayne",
+ "full_name": "John Wayne",
+ "first_name": "John",
+ "last_name": "Wayne",
+ "identity_url": "ardev-tpzed-r09t5ztf5qd3rlj",
+ "is_active": true,
+ "is_admin": null,
+ "is_invited": true,
+ "prefs": {},
+ "writable_by": [
+ "ardev-tpzed-000000000000000",
+ "ardev-tpzed-q6dvn7sby55up1b",
+ "ardev-j7d0g-000000000000000"
+ ]
+}
\ No newline at end of file
--- /dev/null
+{
+ "kind": "arvados#userList",
+ "etag": "",
+ "self_link": "",
+ "offset": 0,
+ "limit": 100,
+ "items": [
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-12389ux30402est",
+ "email": "test.user@email.com",
+ "first_name": "Test",
+ "last_name": "User",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-123vn7sby55up1b",
+ "email": "test.user1@email.com",
+ "first_name": "Test1",
+ "last_name": "User1",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-123g70lq1m3c6fz",
+ "email": "test.user2@email.com",
+ "first_name": "Test2",
+ "last_name": "User2",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-1233zsoudkgq92e",
+ "email": "test.user3@email.com",
+ "first_name": "Test3",
+ "last_name": "User3",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-1234xjvs0clppd3",
+ "email": "test.user4@email.com",
+ "first_name": "Test4",
+ "last_name": "User4",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-123bpggscmn6z8m",
+ "email": "test.user5@email.com",
+ "first_name": "Test5",
+ "last_name": "User5",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-1231uysivaz6ipi",
+ "email": "test.user6@email.com",
+ "first_name": "Test6",
+ "last_name": "User6",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-123b0a1wu0q6cm4",
+ "email": "test.user7@email.com",
+ "first_name": "Test7",
+ "last_name": "User7",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-123bz6n6si24t6v",
+ "email": "test.user8@email.com",
+ "first_name": "Test8",
+ "last_name": "User8",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-123lxhzifligheu",
+ "email": "test.user9@email.com",
+ "first_name": "Test9",
+ "last_name": "User9",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-123gaz31qbopewh",
+ "email": "test.user10@email.com",
+ "first_name": "Test10",
+ "last_name": "User10",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-123dmcf65z973uo",
+ "email": "test.user11@email.com",
+ "first_name": "Test11",
+ "last_name": "User11",
+ "is_active": true
+ },
+ {
+ "kind": "arvados#user",
+ "uuid": "ardev-tpzed-1239y3lj7ybpyg8",
+ "email": "test.user12@email.com",
+ "first_name": "Test12",
+ "last_name": "User12",
+ "is_active": true
+ }
+
+ ],
+ "items_available": 13
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/users/ardev-tpzed-000000000000000",
+ "kind": "arvados#user",
+ "etag": "2ehmra38iwfuexvz1cjno5xua",
+ "uuid": "ardev-tpzed-000000000000000",
+ "owner_uuid": "ardev-tpzed-000000000000000",
+ "created_at": "2016-10-19T07:48:04.838534000Z",
+ "modified_by_client_uuid": null,
+ "modified_by_user_uuid": "ardev-tpzed-000000000000000",
+ "modified_at": "2016-10-19T07:48:04.833164000Z",
+ "email": "root",
+ "username": null,
+ "full_name": "root",
+ "first_name": "root",
+ "last_name": "",
+ "identity_url": null,
+ "is_active": true,
+ "is_admin": true,
+ "is_invited": true,
+ "prefs": {},
+ "writable_by": [
+ "ardev-tpzed-000000000000000"
+ ]
+}
\ No newline at end of file
--- /dev/null
+#!/bin/bash -x
+#
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+#
+set -e
+
+format_last_commit_here() {
+ local format="$1"; shift
+ TZ=UTC git log -n1 --first-parent "--format=format:$format" .
+}
+
+version_from_git() {
+ # Output the version being built, or if we're building a
+ # dev/prerelease, output a version number based on the git log for
+ # the current working directory.
+ if [[ -n "$ARVADOS_BUILDING_VERSION" ]]; then
+ echo "$ARVADOS_BUILDING_VERSION"
+ return
+ fi
+
+ local git_ts git_hash prefix
+ if [[ -n "$1" ]] ; then
+ prefix="$1"
+ else
+ prefix="0.1"
+ fi
+
+ declare $(format_last_commit_here "git_ts=%ct git_hash=%h")
+ ARVADOS_BUILDING_VERSION="$(git describe --abbrev=0).$(date -ud "@$git_ts" +%Y%m%d%H%M%S)"
+ echo "$ARVADOS_BUILDING_VERSION"
+}
+
+nohash_version_from_git() {
+ version_from_git $1 | cut -d. -f1-3
+}
+
+timestamp_from_git() {
+ format_last_commit_here "%ct"
+}
+if [[ -n "$1" ]]; then
+ build_version="$1"
+else
+ build_version="$(version_from_git)"
+fi
+#UID=$(id -u) # UID is read-only on many systems
+exec docker run --rm --user $UID -v $PWD:$PWD -w $PWD gradle /bin/sh -c 'gradle clean && gradle test && gradle jar install '"$gradle_upload"
\ No newline at end of file
"bytes"
"crypto/md5"
"fmt"
+ "io"
+ "io/ioutil"
"log"
"math"
+ "os"
"runtime"
"sort"
"strings"
"sync"
+ "syscall"
"time"
"git.curoverse.com/arvados.git/sdk/go/arvados"
Dumper logrus.FieldLogger
Metrics *metrics
+ LostBlocksFile string
+
*BlockStateMap
KeepServices map[string]*KeepService
DefaultReplication int
errors []error
stats balancerStats
mutex sync.Mutex
+ lostBlocks io.Writer
}
// Run performs a balance operation using the given config and
defer bal.time("sweep", "wall clock time to run one full sweep")()
+ var lbFile *os.File
+ if bal.LostBlocksFile != "" {
+ tmpfn := bal.LostBlocksFile + ".tmp"
+ lbFile, err = os.OpenFile(tmpfn, os.O_CREATE|os.O_WRONLY, 0777)
+ if err != nil {
+ return
+ }
+ defer lbFile.Close()
+ err = syscall.Flock(int(lbFile.Fd()), syscall.LOCK_EX|syscall.LOCK_NB)
+ if err != nil {
+ return
+ }
+ defer func() {
+ // Remove the tempfile only if we didn't get
+ // as far as successfully renaming it.
+ if lbFile != nil {
+ os.Remove(tmpfn)
+ }
+ }()
+ bal.lostBlocks = lbFile
+ } else {
+ bal.lostBlocks = ioutil.Discard
+ }
+
if len(config.KeepServiceList.Items) > 0 {
err = bal.SetKeepServices(config.KeepServiceList)
} else {
if err = bal.CheckSanityLate(); err != nil {
return
}
+ if lbFile != nil {
+ err = lbFile.Sync()
+ if err != nil {
+ return
+ }
+ err = os.Rename(bal.LostBlocksFile+".tmp", bal.LostBlocksFile)
+ if err != nil {
+ return
+ }
+ lbFile = nil
+ }
if runOptions.CommitPulls {
err = bal.CommitPulls(&config.Client)
if err != nil {
s.lost.replicas -= surplus
s.lost.blocks++
s.lost.bytes += bytes * int64(-surplus)
+ fmt.Fprintf(bal.lostBlocks, "%s\n", strings.SplitN(string(result.blkid), "+", 2)[0])
case surplus < 0:
s.underrep.replicas -= surplus
s.underrep.blocks++
"io/ioutil"
"net/http"
"net/http/httptest"
+ "os"
"strings"
"sync"
"time"
return rt
}
+func (s *stubServer) serveKeepstoreIndexFoo1() *reqTracker {
+ rt := &reqTracker{}
+ s.mux.HandleFunc("/index/", func(w http.ResponseWriter, r *http.Request) {
+ rt.Add(r)
+ io.WriteString(w, "acbd18db4cc2f85cedef654fccc4a4d8+3 12345678\n\n")
+ })
+ for _, mounts := range stubMounts {
+ for i, mnt := range mounts {
+ i := i
+ s.mux.HandleFunc(fmt.Sprintf("/mounts/%s/blocks", mnt.UUID), func(w http.ResponseWriter, r *http.Request) {
+ rt.Add(r)
+ if i == 0 {
+ io.WriteString(w, "acbd18db4cc2f85cedef654fccc4a4d8+3 12345678\n\n")
+ } else {
+ io.WriteString(w, "\n")
+ }
+ })
+ }
+ }
+ return rt
+}
+
func (s *stubServer) serveKeepstoreTrash() *reqTracker {
return s.serveStatic("/trash", `{}`)
}
c.Check(pullReqs.Count(), check.Equals, 0)
}
+func (s *runSuite) TestWriteLostBlocks(c *check.C) {
+ lostf, err := ioutil.TempFile("", "keep-balance-lost-blocks-test-")
+ c.Assert(err, check.IsNil)
+ s.config.LostBlocksFile = lostf.Name()
+ defer os.Remove(lostf.Name())
+ opts := RunOptions{
+ CommitPulls: true,
+ CommitTrash: true,
+ Logger: s.logger(c),
+ }
+ s.stub.serveCurrentUserAdmin()
+ s.stub.serveFooBarFileCollections()
+ s.stub.serveKeepServices(stubServices)
+ s.stub.serveKeepstoreMounts()
+ s.stub.serveKeepstoreIndexFoo1()
+ s.stub.serveKeepstoreTrash()
+ s.stub.serveKeepstorePull()
+ srv, err := NewServer(s.config, opts)
+ c.Assert(err, check.IsNil)
+ _, err = srv.Run()
+ c.Check(err, check.IsNil)
+ lost, err := ioutil.ReadFile(lostf.Name())
+ c.Assert(err, check.IsNil)
+ c.Check(string(lost), check.Equals, "37b51d194a7513e45b56f6524f2d51f2\n")
+}
+
func (s *runSuite) TestDryRun(c *check.C) {
opts := RunOptions{
CommitPulls: false,
}
func (s *runSuite) TestCommit(c *check.C) {
+ lostf, err := ioutil.TempFile("", "keep-balance-lost-blocks-test-")
+ c.Assert(err, check.IsNil)
+ s.config.LostBlocksFile = lostf.Name()
+ defer os.Remove(lostf.Name())
+
s.config.Listen = ":"
s.config.ManagementToken = "xyzzy"
opts := RunOptions{
// in a poor rendezvous position
c.Check(bal.stats.pulls, check.Equals, 2)
+ lost, err := ioutil.ReadFile(lostf.Name())
+ c.Assert(err, check.IsNil)
+ c.Check(string(lost), check.Equals, "")
+
metrics := s.getMetrics(c, srv)
c.Check(metrics, check.Matches, `(?ms).*\narvados_keep_total_bytes 15\n.*`)
c.Check(metrics, check.Matches, `(?ms).*\narvados_keepbalance_changeset_compute_seconds_sum [0-9\.]+\n.*`)
// Timeout for outgoing http request/response cycle.
RequestTimeout arvados.Duration
+
+ // Destination filename for the list of lost block hashes, one
+ // per line. Updated atomically during each successful run.
+ LostBlocksFile string
}
// RunOptions controls runtime behavior. The flags/options that belong
func (srv *Server) Run() (*Balancer, error) {
bal := &Balancer{
- Logger: srv.Logger,
- Dumper: srv.Dumper,
- Metrics: srv.metrics,
+ Logger: srv.Logger,
+ Dumper: srv.Dumper,
+ Metrics: srv.metrics,
+ LostBlocksFile: srv.config.LostBlocksFile,
}
var err error
srv.runOptions, err = bal.Run(srv.config, srv.runOptions)
"github.com/prometheus/client_golang/prometheus"
)
-const azureDefaultRequestTimeout = arvados.Duration(10 * time.Minute)
+const (
+ azureDefaultRequestTimeout = arvados.Duration(10 * time.Minute)
+ azureDefaultListBlobsMaxAttempts = 12
+ azureDefaultListBlobsRetryDelay = arvados.Duration(10 * time.Second)
+)
var (
azureMaxGetBytes int
ReadOnly bool
RequestTimeout arvados.Duration
StorageClasses []string
+ ListBlobsRetryDelay arvados.Duration
+ ListBlobsMaxAttempts int
azClient storage.Client
container *azureContainer
// Start implements Volume.
func (v *AzureBlobVolume) Start(vm *volumeMetricsVecs) error {
+ if v.ListBlobsRetryDelay == 0 {
+ v.ListBlobsRetryDelay = azureDefaultListBlobsRetryDelay
+ }
+ if v.ListBlobsMaxAttempts == 0 {
+ v.ListBlobsMaxAttempts = azureDefaultListBlobsMaxAttempts
+ }
if v.ContainerName == "" {
return errors.New("no container name given")
}
Prefix: prefix,
Include: &storage.IncludeBlobDataset{Metadata: true},
}
- for {
- resp, err := v.container.ListBlobs(params)
+ for page := 1; ; page++ {
+ resp, err := v.listBlobs(page, params)
if err != nil {
return err
}
}
}
+// call v.container.ListBlobs, retrying if needed.
+func (v *AzureBlobVolume) listBlobs(page int, params storage.ListBlobsParameters) (resp storage.BlobListResponse, err error) {
+ for i := 0; i < v.ListBlobsMaxAttempts; i++ {
+ resp, err = v.container.ListBlobs(params)
+ err = v.translateError(err)
+ if err == VolumeBusyError {
+ log.Printf("ListBlobs: will retry page %d in %s after error: %s", page, v.ListBlobsRetryDelay, err)
+ time.Sleep(time.Duration(v.ListBlobsRetryDelay))
+ continue
+ } else {
+ break
+ }
+ }
+ return
+}
+
// Trash a Keep block.
func (v *AzureBlobVolume) Trash(loc string) error {
if v.ReadOnly {
}
params := storage.ListBlobsParameters{Include: &storage.IncludeBlobDataset{Metadata: true}}
- for {
- resp, err := v.container.ListBlobs(params)
+ for page := 1; ; page++ {
+ resp, err := v.listBlobs(page, params)
if err != nil {
log.Printf("EmptyTrash: ListBlobs: %v", err)
break
"testing"
"time"
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
"github.com/Azure/azure-sdk-for-go/storage"
"github.com/ghodss/yaml"
"github.com/prometheus/client_golang/prometheus"
type azStubHandler struct {
sync.Mutex
- blobs map[string]*azBlob
- race chan chan struct{}
+ blobs map[string]*azBlob
+ race chan chan struct{}
+ didlist503 bool
}
func newAzStubHandler() *azStubHandler {
rw.WriteHeader(http.StatusAccepted)
case r.Method == "GET" && r.Form.Get("comp") == "list" && r.Form.Get("restype") == "container":
// "List Blobs" API
+ if !h.didlist503 {
+ h.didlist503 = true
+ rw.WriteHeader(http.StatusServiceUnavailable)
+ return
+ }
prefix := container + "|" + r.Form.Get("prefix")
marker := r.Form.Get("marker")
t.Fatal(err)
}
}
+ azClient.Sender = &singleSender{}
bs := azClient.GetBlobService()
v := &AzureBlobVolume{
- ContainerName: container,
- ReadOnly: readonly,
- AzureReplication: replication,
- azClient: azClient,
- container: &azureContainer{ctr: bs.GetContainerReference(container)},
+ ContainerName: container,
+ ReadOnly: readonly,
+ AzureReplication: replication,
+ ListBlobsMaxAttempts: 2,
+ ListBlobsRetryDelay: arvados.Duration(time.Millisecond),
+ azClient: azClient,
+ container: &azureContainer{ctr: bs.GetContainerReference(container)},
}
return &TestableAzureBlobVolume{
for _, v := range vols {
if err := v.IndexTo(prefix, resp); err != nil {
- // The only errors returned by IndexTo are
- // write errors returned by resp.Write(),
- // which probably means the client has
- // disconnected and this error will never be
- // reported to the client -- but it will
- // appear in our own error log.
- http.Error(resp, err.Error(), http.StatusInternalServerError)
+ // We can't send an error message to the
+ // client because we might have already sent
+ // headers and index content. All we can do is
+ // log the error in our own logs, and (in
+ // cases where headers haven't been sent yet)
+ // set a 500 status.
+ //
+ // If headers have already been sent, the
+ // client must notice the lack of trailing
+ // newline as an indication that the response
+ // is incomplete.
+ log.Printf("index error from volume %s: %s", v, err)
+ http.Error(resp, "", http.StatusInternalServerError)
return
}
}
if task.finishtime is None or timestamp > task.finishtime:
task.finishtime = timestamp
- if self.starttime is None or timestamp < task.starttime:
+ if self.starttime is None or timestamp < self.starttime:
self.starttime = timestamp
- if self.finishtime is None or timestamp < task.finishtime:
+ if self.finishtime is None or timestamp > self.finishtime:
self.finishtime = timestamp
if (not self.detected_crunch1) and task.starttime is not None and task.finishtime is not None:
stats['user+sys'] = stats.get('user', 0) + stats.get('sys', 0)
if 'tx' in stats or 'rx' in stats:
stats['tx+rx'] = stats.get('tx', 0) + stats.get('rx', 0)
- for stat, val in stats.items():
- if group == 'interval':
- if stat == 'seconds':
- this_interval_s = val
- continue
- elif not (this_interval_s > 0):
+ if group == 'interval':
+ if 'seconds' in stats:
+ this_interval_s = stats.get('seconds',0)
+ del stats['seconds']
+ if this_interval_s <= 0:
logger.error(
"BUG? interval stat given with duration {!r}".
format(this_interval_s))
- continue
- else:
+ else:
+ logger.error('BUG? interval stat missing duration')
+ for stat, val in stats.items():
+ if group == 'interval' and this_interval_s:
stat = stat + '__rate'
val = val / this_interval_s
if stat in ['user+sys__rate', 'tx+rx__rate']:
projects / arvados.git / commitdiff