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Openalex fetch example #61

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Openalex fetch example #61

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1383a16
added OpenAlex example configuration
bkampe Aug 28, 2024
b57ddec
a bit of cleanup
bkampe Aug 28, 2024
f4e3cc0
added OpenAlex example configuration
bkampe Sep 11, 2024
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -29,3 +29,6 @@ utilities/rdbmigration/.work
**/.classpath
**/.project
**/bin/
/example-scripts/bash-scripts/full-harvest-examples/1.13-1.15-examples/example-openalex/logs/
/example-scripts/bash-scripts/full-harvest-examples/1.13-1.15-examples/example-openalex/data/
/example-scripts/bash-scripts/full-harvest-examples/1.13-1.15-examples/example-openalex/previous-harvest/
Comment on lines +32 to +34
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I was thinking that lines 3-7 includes this case?

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I think that adding:

**/data
**/logs
**/previous-harvest

to root-level .gitignore will solve this issue.

87 changes: 87 additions & 0 deletions ...ripts/full-harvest-examples/1.13-1.15-examples/example-openalex/diff-additions.config.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
<?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
-->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% The diff tool is used to compare jena models and produce a result model which is the first model (minuend) %>
<% with any matching statements in the second model (subtrahend) removed from it. %>
<% ===== %>
<% This tool produces the graph-math difference of the triples between two models. It produces a model with the %>
<% triples which are in the minuend and not in the subtrahend. %>
<% Expressed mathematically as minuend - subtrahend = difference %>
<% Neither the minend nor the subtrahend are altered. %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->
<Task>
<!--INPUT -->
<!--MINUEND : for more information please see the given config file -->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="minuend"> The model described by this config file is the model which has the data which will be in %>
<% output model. %>
<% %>
<% %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->
<Param name="minuend">harvested-data.model.xml</Param>

<!--SUBTRAHEND : for more information please see the given config file -->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="subtrahend"> The model described by this config file contains the triples which are not goning to %>
<% be within the output model. If the triples match any within the minuend model then the output will be smaller %>
<% than the minuend. %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->
<Param name="subtrahend">previous-harvest.model.xml</Param>


<!--DUMPFILE -->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="dumptofile"> This denotes the place for a text dump file to be produced. The default format of the %>
<% dumpfile is RDF/XML and is able to be added or removed from another model through the use of the transfer tool. %>
<% <Param name="dumptolanguage"> This denotes the language the rdf is in. Predefined values for lang are "RDF/XML", %>
<% "N-TRIPLE", "TURTLE" (or "TTL") and "N3". * null represents the default language, "RDF/XML". "RDF/XML-ABBREV" is %>
<% a synonym for "RDF/XML". %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->
<Param name="dumptofile">filename=data/vivo-additions.rdf.xml</Param>

<!--OUTPUT : for more information please see the given config file -->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="output"> The model described by this config file is the model that will be produced which will %>
<% contain the data which is in the minuend but not in the subtrahend. %>
<% %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->

<!-- <Param name="output">diff-output.model.xml</Param> -->

<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="selective-diff"> Tells Diff to use the selectiveDiff method in execute. If any "update-types" %>
<% parameters (below) are set, this flag is implicitly set. This flag exists mostly for the case where one wishes %>
<% to use selectiveDiff without specifying update types. %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->

<!-- <Param name="selective-diff">T</Param> -->

<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="update-types"> Each update-types entry specifies a type allowed to be updated in the process of %>
<% a diff, meant primarily for creating subtraction models. Untested for addition models! %>
<% %>
<% Specifying any type at all will cause Diff to use the selectiveDiff() method, leading to unspecified types %>
<% being preserved. %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->

<!-- <Param name="update-types">http://xmlns.com/foaf/0.1/Person</Param> -->
<Param name="wordiness">INFO</Param>
</Task>
86 changes: 86 additions & 0 deletions ...ts/full-harvest-examples/1.13-1.15-examples/example-openalex/diff-subtractions.config.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
<?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
-->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% The diff tool is used to compare jena models and produce a result model which is the first model (minuend) %>
<% with any matching statements in the second model (subtrahend) removed from it. %>
<% ===== %>
<% This tool produces the graph-math difference of the triples between two models. It produces a model with the %>
<% triples which are in the minuend and not in the subtrahend. %>
<% Expressed mathematically as minuend - subtrahend = difference %>
<% Neither the minend nor the subtrahend are altered. %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->
<Task>
<!--INPUT -->
<!--MINUEND : for more information please see the given config file -->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="minuend"> The model described by this config file is the model which has the data which will be in %>
<% output model. %>
<% %>
<% %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->
<Param name="minuend">previous-harvest.model.xml</Param>

<!--SUBTRAHEND : for more information please see the given config file -->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="subtrahend"> The model described by this config file contains the triples which are not goning to %>
<% be within the output model. If the triples match any within the minuend model then the output will be smaller %>
<% than the minuend. %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->
<Param name="subtrahend">harvested-data.model.xml</Param>

<!--DUMPFILE -->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="dumptofile"> This denotes the place for a text dump file to be produced. The default format of the %>
<% dumpfile is RDF/XML and is able to be added or removed from another model through the use of the transfer tool. %>
<% <Param name="dumptolanguage"> This denotes the language the rdf is in. Predefined values for lang are "RDF/XML", %>
<% "N-TRIPLE", "TURTLE" (or "TTL") and "N3". * null represents the default language, "RDF/XML". "RDF/XML-ABBREV" is %>
<% a synonym for "RDF/XML". %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->
<Param name="dumptofile">filename=data/vivo-subtractions.rdf.xml</Param>

<!--OUTPUT : for more information please see the given config file -->
<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="output"> The model described by this config file is the model that will be produced which will %>
<% contain the data which is in the minuend but not in the subtrahend. %>
<% %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->

<!-- <Param name="output">diff-output.model.xml</Param> -->

<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="selective-diff"> Tells Diff to use the selectiveDiff method in execute. If any "update-types" %>
<% parameters (below) are set, this flag is implicitly set. This flag exists mostly for the case where one wishes %>
<% to use selectiveDiff without specifying update types. %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->

<!-- <Param name="selective-diff">T</Param> -->

<!--
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
<% <Param name="update-types"> Each update-types entry specifies a type allowed to be updated in the process of %>
<% a diff, meant primarily for creating subtraction models. Untested for addition models! %>
<% %>
<% Specifying any type at all will cause Diff to use the selectiveDiff() method, leading to unspecified types %>
<% being preserved. %>
<% ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %>
-->

<!-- <Param name="update-types">http://xmlns.com/foaf/0.1/Person</Param> -->
<Param name="wordiness">INFO</Param>
</Task>
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