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DD-1965 Add packaging format extension (#11)
When creating a storage root, copy the packaging-format-registry and property-registry extensions to its extensions directory. When adding a new version of an object, update the object-version-properties with a hard-coded (for now) packaging-format = DANS RDA BagPack Profile/0.1.0 property. Upgraded dans-ocfl-java-extensions and dans-layer-store-lib dependencies, so that the files in the extension folder are now also backed by the database and can therefore be retrieved faster. This is necessary for updating object-version-properties to be feasible.
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‎pom.xml‎

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</parent>
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<artifactId>dd-data-vault</artifactId>
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<version>0.9.1-SNAPSHOT</version>
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<version>0.10.0-SNAPSHOT</version>
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<name>DD Data Vault</name>
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<url>https://github.com/DANS-KNAW/dd-data-vault</url>
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<dependency>
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<groupId>nl.knaw.dans</groupId>
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<artifactId>dans-ocfl-java-extensions-lib</artifactId>
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<version>0.5.0</version>
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</dependency>
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<dependency>
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<groupId>io.ocfl</groupId>

‎src/main/assembly/dist/cfg/config.yml‎

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#
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ocflRepository:
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workDir: /data/vault/tmp
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rootExtensionsSourcePath: /etc/opt/dans.knaw.nl/dd-data-vault/ocfl-root-extensions
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#
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# Default version information to be used when no version information is provided when adding an object version. Currently, there is no way to

‎src/main/assembly/dist/cfg/ocfl-root-extensions/packaging-format-registry/7e33ca1db30a5e8a00f5ad0c0529509e/Research Data Repository Interoperability.pdf‎

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‎src/main/assembly/dist/cfg/ocfl-root-extensions/packaging-format-registry/7e33ca1db30a5e8a00f5ad0c0529509e/dans-bagpack-profile-0.1.0.md‎

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DANS BagPack Profile v0.1.0
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===========================
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Introduction
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------------
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### Version
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* Document version: 0.1.0
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* Publication date: N/A
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### Status
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The status of this document is DRAFT.
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### Scope
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This document specifies what constitutes a DANS BagPack in its most simple form. This version of the document is a preliminary release. The requirements in it
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are non-normative and therefore formulated as "SHOULD"-rules. BagPacks that declare themselves as following the DANS BagPack Profile v0.1.0 are a best effort
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and are not validated.
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### Overview and Conventions
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#### Keywords
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The keywords "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be
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interpreted as described in [RFC 2119]{:target=_blank}.
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The key word "SHOULD" is also used to specify requirements that are impossible or impractical to check by the archival organization (i.e. DANS). The client
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should do its best to meet these requirements, but not rely on their being validated by the archival organization.
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#### Subdivisions
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The requirements are subdivided into the following sections:
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* RDA BagPack Related - requirements that refer back to the [RDA BagPack]{:target=_blank} specifications. If a bag only needs to comply with the RDA BagPack
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specifications, then it should be sufficient to only check this section.
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* Extra Requirements for DANS BagPack - requirements that are specific to the DANS BagPack Profile, and which are in addition to the RDA BagPack requirements.
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The sections are numbered and may have numbered subsections. The requirements themselves are stated as numbered rules. Rules may have parts that are labeled
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with letters: (a), (b), (c), etc. To uniquely identify a specific rule, use the notation
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```
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<section-nr>[.<subsection-nr>].<rule-nr> [(<letter>)]
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```
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Example: `2.3.4 (e)` means part **e** of the fourth rule in subsection 3 of section 2.
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Requirements
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------------
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### 1. RDA BagPack Related
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The following items are required by the [RDA BagPack]{:target=_blank} specifications:
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1. A DANS BagPack SHOULD be valid according to [BagIt v1.0]{:target=_blank}.
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2. A DANS BagPack SHOULD contain a file `metadata/datacite.xml` (a) this file SHOULD be valid according to the
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[DataCite schema version 4.0 or later]{:target=_blank}, except for the requirement that there MUST be a DOI present: a DOI is not required for a DANS
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BagPack; (b) [DataCite's recommended properties]{:target=_blank} SHOULD be present.
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3. Other files besides `datacite.xml` MAY be present in the `metadata` folder.
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4. The files in the `metadata` folder SHOULD be mentioned in the `tag-manifest` (this is optional in BagIt, but required by RDA BagPack).
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5. `BagIt-Profile-Identifier` SHOULD be provided.
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### 2. Extra Requirements for DANS BagPack
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The following items are required by the DANS BagPack Profile, in addition to the requirements of RDA BagPack:
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1. `BagIt-Profile-Identifier` SHOULD contain `https://doi.org/10.17026/e948-0r32`.
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2. There SHOULD be a file called `metadata/pid-mapping.txt`.
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3. There SHOULD be a file called `metadata/oai-ore.jsonld`.
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[RFC 2119]: {{ rfc_2119 }}
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[BagIt v1.0]: {{ bagit }}
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[RDA BagPack]: {{ rda_bagpack }}
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[DataCite schema version 4.0 or later]: {{ datacite_4_0 }}
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[DANS BagPack BagIt Profile]: {{ dans_bagpack_bagit_profile }}
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[DataCite's recommended properties]: {{ levels_of_obligation }}

‎src/main/assembly/dist/cfg/ocfl-root-extensions/packaging-format-registry/7e33ca1db30a5e8a00f5ad0c0529509e/dans-bagpack-profile-1.0.0.json‎

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{
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"BagIt-Profile-Info": {
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"BagIt-Profile-Identifier": "https://doi.org/10.17026/e948-0r32",
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"Source-Organization": "dans.knaw.nl",
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"Contact-Name": "DANS-KNAW",
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"Contact-Email": "info@dans.knaw.nl",
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"External-Description": "DANS BagPack Profile",
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"Version": "1.0.0"
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},
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"Bag-Info": {
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"Bagging-Date": {
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"required": true
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},
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"Source-Organization": {
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"required": false
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},
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"Contact-Name": {
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"required": true
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},
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"Contact-Phone": {
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"required": false
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},
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"Contact-Email": {
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"required": true
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},
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"External-Identifier": {
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"required": true
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},
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"External-Description": {
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"required": false
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},
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"Bag-Size": {
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"required": true
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},
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"Payload-Oxum": {
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"required": true
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},
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"Source-Identifier": {
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"required": false
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}
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},
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"Manifests-Required": [
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"sha1"
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],
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"Allow-Fetch.txt": false,
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"Serialization": "optional",
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"Accept-Serialization": [
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"application/zip",
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"application/tar",
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"application/tar+gzip"
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],
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"Accept-BagIt-Version": [
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"1.0"
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],
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"Tag-Manifests-Required": [
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"sha1"
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],
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"Tag-Files-Required": [
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"metadata/datacite.xml",
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"metadata/pid-mapping.txt",
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"metadata/oai-ore.jsonld"
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]
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}

‎src/main/assembly/dist/cfg/ocfl-root-extensions/packaging-format-registry/config.json‎

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{
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"extensionName": "packaging-format-registry",
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"packagingFormatDigestAlgorithm": "md5",
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"digestAlgorithm": "sha512"
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}

‎src/main/assembly/dist/cfg/ocfl-root-extensions/packaging-format-registry/packaging_format_inventory.json‎

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{
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"manifest": {
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"7e33ca1db30a5e8a00f5ad0c0529509e": {
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"name": "DANS RDA BagPack Profile",
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"version": "0.1.0",
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"summary": "Extension of the RDA BagPack Profile for DANS"
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}
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}
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}

‎src/main/assembly/dist/cfg/ocfl-root-extensions/packaging-format-registry/packaging_format_inventory.json.sha512‎

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94384db8fc982e39d9d9006718342db91a1718c19f7da759a8ca2f9e5ac2418ce54fabbeb2b1a0c41f0401373e5b85c4727fe30d5c2216df203bce40d6b12774 packaging_format_inventory.json
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‎src/main/assembly/dist/cfg/ocfl-root-extensions/property-registry/config.json‎

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{
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"extensionName": "property-registry",
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"propertyRegistry": {
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"packaging-format": {
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"description": "The packaging format of the current object version, as defined in the packaging-format-registry extension.",
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"type": "string",
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"required": true
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}
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}
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}

‎src/main/java/nl/knaw/dans/datavault/DdDataVaultApplication.java‎

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var itemStore = new LayeredItemStore(dao, layerManager, new StoreInventoryDbBackedContentManager());
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var ocflRepositoryProvider = createUnitOfWorkAwareProxy(OcflRepositoryProvider.builder()
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.itemStore(itemStore)
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.rootExtensionsSourcePath(configuration.getDataVault().getOcflRepository().getRootExtensionsSourcePath())
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.defaultVersionInfoConfig(configuration.getDataVault().getDefaultVersionInfo())
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.workDir(configuration.getDataVault().getOcflRepository().getWorkDir())
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.build());

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