- npm updates for webpack-encore and postcss-loader - DatasetExtension.ts: use relation contributors for PersonContributor - added DoiClient.ts and DoiClientContract.ts - rozes.ts: addes routes for creating and storing doi identifier - addes xslt doi_datacite.xslt needed for registering DOI identifier
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22 changed files with 1836 additions and 677 deletions
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@ -2,6 +2,7 @@ import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
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import { Client } from '@opensearch-project/opensearch';
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import User from 'App/Models/User';
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import Dataset from 'App/Models/Dataset';
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import DatasetIdentifier from 'App/Models/DatasetIdentifier';
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import XmlModel from 'App/Library/XmlModel';
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import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
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import { create } from 'xmlbuilder2';
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@ -10,6 +11,12 @@ import { transform } from 'saxon-js';
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import type { ModelQueryBuilderContract } from '@ioc:Adonis/Lucid/Orm';
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import { schema, CustomMessages } from '@ioc:Adonis/Core/Validator';
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import { DateTime } from 'luxon';
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import Index from 'App/Library/Utils/Index';
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import { getDomain } from 'App/Utils/utility-functions';
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import { DoiClient } from 'App/Library/Doi/DoiClient';
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import DoiClientException from 'App/Exceptions/DoiClientException';
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import Logger from '@ioc:Adonis/Core/Logger';
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import { HttpException } from 'node-exceptions';
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// Create a new instance of the client
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const client = new Client({ node: 'http://localhost:9200' }); // replace with your OpenSearch endpoint
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@ -66,6 +73,7 @@ export default class DatasetsController {
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.where('editor_id', user.id)
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.doesntHave('identifier', 'and');
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})
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// .preload('identifier')
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.preload('titles')
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.preload('user', (query) => query.select('id', 'login'))
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.preload('editor', (query) => query.select('id', 'login'))
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@ -273,13 +281,79 @@ export default class DatasetsController {
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dataset.publisher_name = publisherName;
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if (await dataset.save()) {
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const index_name = 'tethys-records';
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await Index.indexDocument(dataset, index_name);
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return response.toRoute('editor.dataset.list').flash('message', 'You have successfully published the dataset!');
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}
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}
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public async create({}: HttpContextContract) {}
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public async doiCreate({ request, inertia }: HttpContextContract) {
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const id = request.param('id');
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const dataset = await Dataset.query()
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.where('id', id)
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.preload('titles')
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.preload('descriptions')
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// .preload('identifier')
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.preload('authors')
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.firstOrFail();
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return inertia.render('Editor/Dataset/Doi', {
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dataset,
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});
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}
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public async store({}: HttpContextContract) {}
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public async doiStore({ request, response }: HttpContextContract) {
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const dataId = request.param('publish_id');
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const dataset = await Dataset.query()
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// .preload('xmlCache')
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.where('publish_id', dataId)
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.firstOrFail();
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const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string;
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let prefix = '';
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let base_domain = '';
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const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
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if (datacite_environment === 'debug') {
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prefix = process.env.DATACITE_TEST_PREFIX || '';
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base_domain = process.env.TEST_BASE_DOMAIN || '';
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} else if (datacite_environment === 'production') {
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prefix = process.env.DATACITE_PREFIX || '';
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base_domain = process.env.BASE_DOMAIN || '';
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}
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// register DOI:
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const doiValue = prefix + '/tethys.' + dataset.publish_id; //'10.21388/tethys.213'
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const landingPageUrl = 'https://doi.' + getDomain(base_domain) + '/' + prefix + '/tethys.' + dataset.publish_id; //https://doi.dev.tethys.at/10.21388/tethys.213
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const doiClient = new DoiClient();
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const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl);
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if (dataciteResponse?.status === 201) {
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// if response OK 201; save the Identifier value into db
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const doiIdentifier = new DatasetIdentifier();
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doiIdentifier.value = doiValue;
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doiIdentifier.dataset_id = dataset.id;
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doiIdentifier.type = 'doi';
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doiIdentifier.status = 'findable';
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// save modified date of datset for re-caching model in db an update the search index
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dataset.server_date_modified = DateTime.now();
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// save updated dataset to db an index to OpenSearch
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try {
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await dataset.related('identifier').save(doiIdentifier);
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const index_name = 'tethys-records';
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await Index.indexDocument(dataset, index_name);
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} catch (error) {
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Logger.error(`${__filename}: Indexing document ${dataset.id} failed: ${error.message}`);
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// Log the error or handle it as needed
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throw new HttpException(error.message);
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}
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return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!');
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} else {
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const message = `Unexpected DataCite MDS response code ${dataciteResponse?.status}`;
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// Log the error or handle it as needed
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throw new DoiClientException(dataciteResponse?.status, message);
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}
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// return response.toRoute('editor.dataset.list').flash('message', xmlMeta);
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}
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public async show({}: HttpContextContract) {}
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@ -404,8 +478,6 @@ export default class DatasetsController {
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public async destroy({}: HttpContextContract) {}
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public async syncOpensearch({}: HttpContextContract) {}
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private async createXmlRecord(dataset: Dataset, datasetNode: XMLBuilder) {
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const domNode = await this.getDatasetXmlDomNode(dataset);
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if (domNode) {
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110
app/Controllers/Http/Editor/deleteDoiMetadata.xml
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110
app/Controllers/Http/Editor/deleteDoiMetadata.xml
Normal file
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@ -0,0 +1,110 @@
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
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<root>
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<Dataset>
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<Rdr_Dataset Id="306" PublisherName="GeoSphere Austria" PublishId="213"
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CreatingCorporation="Tethys RDR" Language="en" ServerState="published"
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Type="measurementdata">
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<CreatedAt Year="2023" Month="11" Day="30" Hour="10" Minute="20" Second="58"
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UnixTimestamp="1701336058" Timezone="Europe/Berlin" />
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<ServerDateModified Year="2024" Month="1" Day="22" Hour="12" Minute="28" Second="17"
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UnixTimestamp="1705922897" Timezone="Europe/Berlin" />
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<ServerDatePublished Year="2024" Month="1" Day="22" Hour="12" Minute="28" Second="8"
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UnixTimestamp="1705922888" Timezone="Europe/Berlin" />
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<TitleMain Id="682" DocumentId="306" Type="Main" Value="rewerewr" Language="en" />
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<TitleAbstract Id="1017" DocumentId="306" Type="Abstract" Value="rewrewr" Language="en" />
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<Licence Id="1" Active="true"
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LinkLicence="https://creativecommons.org/licenses/by/4.0/deed.en"
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LinkLogo="https://licensebuttons.net/l/by/4.0/88x31.png"
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NameLong="Creative Commons Attribution 4.0 International (CC BY 4.0)"
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Name="CC-BY-4.0" SortOrder="1" />
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<PersonAuthor Id="1" Email="m.moser@univie.ac.at" FirstName="Michael" LastName="Moser"
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Status="true" NameType="Personal" Role="author" SortOrder="1"
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AllowEmailContact="false" />
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<PersonContributor Id="28" Email="juergen.reitner@geologie.ac.at" FirstName="Jürgen"
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LastName="Reitner" Status="false" NameType="Personal" Role="contributor"
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SortOrder="1" AllowEmailContact="false" />
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<Subject Id="143" Language="de" Type="Geoera" Value="Aletshausen-Langenneufnach Störung"
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CreatedAt="2023-11-21 17:17:43" UpdatedAt="2023-11-21 17:17:43" />
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<Subject Id="164" Language="de" Type="Geoera" Value="Wolfersberg-Moosach Störung"
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ExternalKey="https://data.geoscience.earth/ncl/geoera/hotLime/faults/3503"
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CreatedAt="2023-11-30 10:20:58" UpdatedAt="2023-11-30 10:20:58" />
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<Subject Id="165" Language="en" Type="Uncontrolled" Value="wefwef"
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CreatedAt="2023-11-30 10:20:58" UpdatedAt="2023-11-30 10:20:58" />
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<File Id="1037" DocumentId="306" PathName="files/306/file-clpkzkkgq0001nds14fua5um6.png"
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Label="freieIP.png" MimeType="image/png" FileSize="112237" VisibleInFrontdoor="true"
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VisibleInOai="true" SortOrder="0" CreatedAt="2023-11-30 10:21:14"
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UpdatedAt="2023-11-30 10:21:14" />
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<Coverage Id="284" DatasetId="306" XMin="11.71142578125" XMax="14.414062500000002"
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YMin="46.58906908309185" YMax="47.45780853075031" CreatedAt="2023-11-30 10:20:58"
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UpdatedAt="2023-11-30 10:20:58" />
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<Collection Id="21" RoleId="3" Number="551" Name="Geology, hydrology, meteorology"
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ParentId="20" Visible="true" VisiblePublish="true" />
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</Rdr_Dataset>
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</Dataset>
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</root>
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<?xml version="1.0" encoding="utf-8"?>
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<resource xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns="http://datacite.org/schema/kernel-4"
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xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.3/metadata.xsd">
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<identifier identifierType="DOI">10.21388/tethys.213</identifier>
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<creators>
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<creator>
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<creatorName nameType="Personal">Moser, Michael</creatorName>
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<givenName>Michael</givenName>
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<familyName>Moser</familyName>
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<affiliation>GBA</affiliation>
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</creator>
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</creators>
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<titles>
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<title xml:lang="en">rewerewr</title>
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</titles>
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<publisher>Tethys RDR</publisher>
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<publicationYear>2024</publicationYear>
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<subjects>
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<subject xml:lang="de">Aletshausen-Langenneufnach Störung</subject>
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<subject xml:lang="de">Wolfersberg-Moosach Störung</subject>
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<subject xml:lang="en">wefwef</subject>
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</subjects>
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<language>en</language>
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<contributors>
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<contributor contributorType="RegistrationAuthority">
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<contributorName>Jürgen Reitner</contributorName>
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</contributor>
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</contributors>
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<dates>
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<date dateType="Created">2023-11-30</date>
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</dates>
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<version>1</version>
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<resourceType resourceTypeGeneral="Dataset">Dataset</resourceType>
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<alternateIdentifiers>
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<alternateIdentifier alternateIdentifierType="url">https://www.tethys.at/dataset/213</alternateIdentifier>
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</alternateIdentifiers>
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<rightsList>
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<rights xml:lang="" rightsURI="https://creativecommons.org/licenses/by/4.0/deed.en"
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schemeURI="https://spdx.org/licenses/" rightsIdentifierScheme="SPDX"
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rightsIdentifier="CC-BY-4.0">Creative Commons Attribution 4.0 International (CC BY 4.0)</rights>
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<rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
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</rightsList>
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<sizes>
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<size>1 datasets</size>
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</sizes>
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<formats>
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<format>image/png</format>
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</formats>
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<descriptions>
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<description xml:lang="en" descriptionType="Abstract">rewrewr</description>
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</descriptions>
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<geoLocations>
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<geoLocation>
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<geoLocationBox>
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<westBoundLongitude>11.71142578125</westBoundLongitude>
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<eastBoundLongitude>14.414062500000002</eastBoundLongitude>
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<southBoundLatitude>46.58906908309185</southBoundLatitude>
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<northBoundLatitude>47.45780853075031</northBoundLatitude>
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</geoLocationBox>
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</geoLocation>
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</geoLocations>
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</resource>
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