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example-scripts/bash-scripts/full-harvest-examples/1.6-examples/example-csv/README
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| You need to modify certains files to ingest data using this example. | ||
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| Here are the files that need to be modified: | ||
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| 1. vivo.model.xml | ||
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| check that the database information is configured correctly for your system. By default, it will | ||
| connect to a database called vitrodb_test on localhost | ||
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| 2. run-csv.sh | ||
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| set to the directory where the harvester was installed | ||
| HARVESTER_INSTALL_DIR | ||
| (Note: there may be other shell scripts which have a set HARVESTER_INSTALL_DIR which | ||
| will need to modified) | ||
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| 3. csvtojdbc.config.xml | ||
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| change inputFile name to your csv data source | ||
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| 5. all the changenamespace-*.config.xml files | ||
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| change the "newNamespace" value to the namespace of your VIVO instance | ||
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...pts/full-harvest-examples/1.6-examples/example-csv/changenamespace-departments.config.xml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!-- | ||
| Copyright (c) 2010-2011 VIVO Harvester Team. For full list of contributors, please see the AUTHORS file provided. | ||
| All rights reserved. | ||
| This program and the accompanying materials are made available under the terms of the new BSD license which accompanies this distribution, and is available at http://www.opensource.org/licenses/bsd-license.html | ||
| --> | ||
| <!-- | ||
| <% Changenamespace is a tool to change the uri of the incoming data to a generated uri of the associated vivo. %> | ||
| <% ===== %> | ||
| <% The generated uri will be in the base name space of the vivo with a unique identifying number. This tool is %> | ||
| <% the way new resources are prepared to be added to a vivo. The actual adding of resources happens with the use %> | ||
| <% of the transfer tool. %> | ||
| --> | ||
| <Task> | ||
| <!--INPUT : for more information please see the given config file --> | ||
| <!-- | ||
| <% <Param name="inputModel">The input model is the jena model which stores the recently harvested information %> | ||
| <% which will be altered by the changenamespace tool. %> | ||
| --> | ||
| <Param name="inputModel">harvested-data.model.xml</Param> | ||
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| <!--VIVO : for more information please see the given config file --> | ||
| <!-- | ||
| <% <Param name="vivoModel"> The vivo model points to the model within vivo which is used as a reference to ensure %> | ||
| <% the new uri doesn't exist already and cause an issue if imported to that vivo instance. %> | ||
| --> | ||
| <Param name="vivoModel">vivo.model.xml</Param> | ||
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| <!-- OPTIONS --> | ||
| <!-- | ||
| <% <Param name="oldNamespace"> This refers to the namespace being switched from. It operates as a filter on the %> | ||
| <% harvested data in order to be sure that only the chosen namspace is being altered %> | ||
| <% <Param name="newNamespace"> The namespace put here should agree with the namespace of the vivo being harvested %> | ||
| <% into. %> | ||
| --> | ||
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| <Param name="oldNamespace">http://vivoweb.org/harvest/csvfile/org/</Param> | ||
| <Param name="newNamespace">http://vivo.sample.edu/individual/</Param> | ||
| <!-- | ||
| <% <Param name="errorLogging"> This parameter determines if a change in namespace will produce an error message. If %> | ||
| <% a change in the namespace should not be happening then this flag should be enabled. %> | ||
| <% %> | ||
| --> | ||
| <!-- <Param name="errorLogging">true</Param> --> | ||
| <Param name="wordiness">INFO</Param> | ||
| </Task> |
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...-scripts/full-harvest-examples/1.6-examples/example-csv/changenamespace-people.config.xml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!-- | ||
| Copyright (c) 2010-2011 VIVO Harvester Team. For full list of contributors, please see the AUTHORS file provided. | ||
| All rights reserved. | ||
| This program and the accompanying materials are made available under the terms of the new BSD license which accompanies this distribution, and is available at http://www.opensource.org/licenses/bsd-license.html | ||
| --> | ||
| <!-- | ||
| <% Changenamespace is a tool to change the uri of the incoming data to a generated uri of the associated vivo. %> | ||
| <% ===== %> | ||
| <% The generated uri will be in the base name space of the vivo with a unique identifying number. This tool is %> | ||
| <% the way new resources are prepared to be added to a vivo. The actual adding of resources happens with the use %> | ||
| <% of the transfer tool. %> | ||
| --> | ||
| <Task> | ||
| <!--INPUT : for more information please see the given config file --> | ||
| <!-- | ||
| <% <Param name="inputModel">The input model is the jena model which stores the recently harvested information %> | ||
| <% which will be altered by the changenamespace tool. %> | ||
| --> | ||
| <Param name="inputModel">harvested-data.model.xml</Param> | ||
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| <!--VIVO : for more information please see the given config file --> | ||
| <!-- | ||
| <% <Param name="vivoModel"> The vivo model points to the model within vivo which is used as a reference to ensure %> | ||
| <% the new uri doesn't exist already and cause an issue if imported to that vivo instance. %> | ||
| --> | ||
| <Param name="vivoModel">vivo.model.xml</Param> | ||
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| <!-- OPTIONS --> | ||
| <!-- | ||
| <% <Param name="oldNamespace"> This refers to the namespace being switched from. It operates as a filter on the %> | ||
| <% harvested data in order to be sure that only the chosen namspace is being altered %> | ||
| <% <Param name="newNamespace"> The namespace put here should agree with the namespace of the vivo being harvested %> | ||
| <% into. %> | ||
| --> | ||
| <Param name="oldNamespace">http://vivoweb.org/harvest/csvfile/person/</Param> | ||
| <Param name="newNamespace">http://vivo.sample.edu/individual/</Param> | ||
| <!-- | ||
| <% <Param name="errorLogging"> This parameter determines if a change in namespace will produce an error message. If %> | ||
| <% a change in the namespace should not be happening then this flag should be enabled. %> | ||
| <% %> | ||
| --> | ||
| <!-- <Param name="errorLogging">true</Param> --> | ||
| <Param name="wordiness">INFO</Param> | ||
| </Task> |
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...ripts/full-harvest-examples/1.6-examples/example-csv/changenamespace-positions.config.xml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!-- | ||
| Copyright (c) 2010-2011 VIVO Harvester Team. For full list of contributors, please see the AUTHORS file provided. | ||
| All rights reserved. | ||
| This program and the accompanying materials are made available under the terms of the new BSD license which accompanies this distribution, and is available at http://www.opensource.org/licenses/bsd-license.html | ||
| --> | ||
| <!-- | ||
| <% Changenamespace is a tool to change the uri of the incoming data to a generated uri of the associated vivo. %> | ||
| <% ===== %> | ||
| <% The generated uri will be in the base name space of the vivo with a unique identifying number. This tool is %> | ||
| <% the way new resources are prepared to be added to a vivo. The actual adding of resources happens with the use %> | ||
| <% of the transfer tool. %> | ||
| --> | ||
| <Task> | ||
| <!--INPUT : for more information please see the given config file --> | ||
| <!-- | ||
| <% <Param name="inputModel">The input model is the jena model which stores the recently harvested information %> | ||
| <% which will be altered by the changenamespace tool. %> | ||
| --> | ||
| <Param name="inputModel">harvested-data.model.xml</Param> | ||
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| <!--VIVO : for more information please see the given config file --> | ||
| <!-- | ||
| <% <Param name="vivoModel"> The vivo model points to the model within vivo which is used as a reference to ensure %> | ||
| <% the new uri doesn't exist already and cause an issue if imported to that vivo instance. %> | ||
| --> | ||
| <Param name="vivoModel">vivo.model.xml</Param> | ||
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| <!-- OPTIONS --> | ||
| <!-- | ||
| <% <Param name="oldNamespace"> This refers to the namespace being switched from. It operates as a filter on the %> | ||
| <% harvested data in order to be sure that only the chosen namspace is being altered %> | ||
| <% <Param name="newNamespace"> The namespace put here should agree with the namespace of the vivo being harvested %> | ||
| <% into. %> | ||
| --> | ||
| <Param name="oldNamespace">http://vivoweb.org/harvest/csvfile/position/</Param> | ||
| <Param name="newNamespace">http://vivo.sample.edu/individual/</Param> | ||
| <!-- | ||
| <% <Param name="errorLogging"> This parameter determines if a change in namespace will produce an error message. If %> | ||
| <% a change in the namespace should not be happening then this flag should be enabled. %> | ||
| <% %> | ||
| --> | ||
| <!-- <Param name="errorLogging">true</Param> --> | ||
| <Param name="wordiness">INFO</Param> | ||
| </Task> |
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...ts/full-harvest-examples/1.6-examples/example-csv/changenamespace-timeinterval.config.xml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!-- | ||
| Copyright (c) 2010-2011 VIVO Harvester Team. For full list of contributors, please see the AUTHORS file provided. | ||
| All rights reserved. | ||
| This program and the accompanying materials are made available under the terms of the new BSD license which accompanies this distribution, and is available at http://www.opensource.org/licenses/bsd-license.html | ||
| --> | ||
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| <Config> | ||
| <Param name="wordiness">INFO</Param> | ||
| <Param name="inputModel">harvested-data.model.xml</Param> | ||
| <Param name="vivoModel">vivo.model.xml</Param> | ||
| <Param name="oldNamespace">http://vivoweb.org/harvest/csvfile/timeInterval/</Param> | ||
| <Param name="newNamespace">http://vivo.sample.edu/individual/</Param> | ||
| <Param name="errorLogging">true</Param> | ||
| </Config> |
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...h-scripts/full-harvest-examples/1.6-examples/example-csv/changenamespace-vcard.config.xml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!-- | ||
| Copyright (c) 2010-2011 VIVO Harvester Team. For full list of contributors, please see the AUTHORS file provided. | ||
| All rights reserved. | ||
| This program and the accompanying materials are made available under the terms of the new BSD license which accompanies this distribution, and is available at http://www.opensource.org/licenses/bsd-license.html | ||
| --> | ||
| <!-- | ||
| <% Changenamespace is a tool to change the uri of the incoming data to a generated uri of the associated vivo. %> | ||
| <% ===== %> | ||
| <% The generated uri will be in the base name space of the vivo with a unique identifying number. This tool is %> | ||
| <% the way new resources are prepared to be added to a vivo. The actual adding of resources happens with the use %> | ||
| <% of the transfer tool. %> | ||
| --> | ||
| <Task> | ||
| <!--INPUT : for more information please see the given config file --> | ||
| <!-- | ||
| <% <Param name="inputModel">The input model is the jena model which stores the recently harvested information %> | ||
| <% which will be altered by the changenamespace tool. %> | ||
| --> | ||
| <Param name="inputModel">harvested-data.model.xml</Param> | ||
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| <!--VIVO : for more information please see the given config file --> | ||
| <!-- | ||
| <% <Param name="vivoModel"> The vivo model points to the model within vivo which is used as a reference to ensure %> | ||
| <% the new uri doesn't exist already and cause an issue if imported to that vivo instance. %> | ||
| --> | ||
| <Param name="vivoModel">vivo.model.xml</Param> | ||
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| <!-- OPTIONS --> | ||
| <!-- | ||
| <% <Param name="oldNamespace"> This refers to the namespace being switched from. It operates as a filter on the %> | ||
| <% harvested data in order to be sure that only the chosen namspace is being altered %> | ||
| <% <Param name="newNamespace"> The namespace put here should agree with the namespace of the vivo being harvested %> | ||
| <% into. %> | ||
| --> | ||
| <Param name="oldNamespace">http://vivoweb.org/harvest/csvfile/vcard/</Param> | ||
| <Param name="newNamespace">http://vivo.sample.edu/individual/</Param> | ||
| <!-- | ||
| <% <Param name="errorLogging"> This parameter determines if a change in namespace will produce an error message. If %> | ||
| <% a change in the namespace should not be happening then this flag should be enabled. %> | ||
| <% %> | ||
| --> | ||
| <!-- <Param name="errorLogging">true</Param> --> | ||
| <Param name="wordiness">INFO</Param> | ||
| </Task> |
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