Ogs subdomains

tools/ogs/.shed.yml

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+name: suite_ogs
+owner: ufz
+description: A suite of tools for OpenGeoSys (ogs)
+long_description: |
+     A suite of tools for ogs
+categories:
+- Geo Science
+remote_repository_url: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/
+homepage_url: https://gitlab.opengeosys.org/ogs/ogs
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: A suite of tools for OpenGeoSys (ogs)
+suite:
+  name: suite_ogs
+  description: A suite of tools for ogs
+  long_description: |
+     A suite of tools for ogs

tools/ogs/identifySubdomains.xml

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+<tool id="ogs_identifysubdomains" name="OGS IdentifySubdomains" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Annotate subdomain meshes with bulk node and element IDs
+    </description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <expand macro="ogs_requirement"/>
+    </requirements>
+        <expand macro="creator"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #import re 
+
+        ln -s '$bulk_mesh' input.vtu &&
+        #for $file in $subdomain_meshes:
+            #set $identifier= re.sub(r'[^\w\-.]', '_', $file.element_identifier)
+            ln -s '$file' '$identifier' &&
+        #end for
+
+        identifySubdomains -m input.vtu -s $search_length -o output_ -- 
+        #for $file in  $subdomain_meshes:
+            #set $identifier= re.sub(r'[^\w\-.]', '_', $file.element_identifier)
+            '$identifier' 
+        #end for  
+    ]]></command>
+    <inputs>
+        <param name="bulk_mesh" type="data" format="vtkxml" label="Bulk Mesh File" help="The bulk mesh file in VTU format."/>
+        <param name="subdomain_meshes" type="data" format="vtkxml" multiple="true" label="Subdomain Mesh Files" help="One or more subdomain mesh files in VTU format."/>
+        <param name="search_length" type="float" min="1e-16" max="10.0" label="Search Length" help="Search radius for the node search algorithm."/>
+    </inputs>
+    <outputs>
+        <data name="output_mesh" format="vtkxml" label="Annotated Subdomain Meshes" from_work_dir="output_quater_circle.vtu"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bulk_mesh" value="disc_with_hole.vtu"/>
+            <param name="subdomain_meshes" value="quater_circle.vtu"/>
+            <param name="search_length" value="1e-06"/>
+            <output name="output_mesh" file="output_quater_circle.vtu"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **Overview:**
+
+        This tool checks if subdomain meshes are part of a given bulk mesh and annotates them with bulk node and element IDs. The results are written to new subdomain mesh files with the specified output prefix.
+
+        **Inputs:**
+        1. **Bulk Mesh File:** The primary bulk mesh file in VTU format.
+        2. **Subdomain Mesh Files:** One or more subdomain mesh files in VTU format.
+        3. **Search Length:** The radius for the node search algorithm.
+
+        **Outputs:**
+        - Annotated Subdomain Meshes: The subdomain meshes annotated with bulk node and element IDs.
+    ]]></help>
+    <expand macro="ogs_citation"/>
+</tool>

tools/ogs/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">6.5.3</token>
+    <token name="@PROFILE@">23.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+    <xml name="ogs_requirement">
+            <requirement type="package" version="@TOOL_VERSION@">ogs</requirement>
+            <yield/>
+    </xml>
+
+    <xml name="ogs_citation">
+        <citations> 
+            <citation type="doi">10.5281/zenodo.13685289</citation>
+        </citations>
+    </xml>
+
+    <xml name="creator">
+        <creator>
+            <organization name="Helmholtz Centre for Environmental Research - UFZ" url ="https://www.ufz.de/"/>
+        </creator>
+    </xml>
+</macros>

tools/ogs/test-data/output_quater_circle.vtu

@@ -0,0 +1,24 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="1.0" byte_order="LittleEndian" header_type="UInt64">
+  <UnstructuredGrid>
+    <Piece NumberOfPoints="31"                   NumberOfCells="30"                  >
+      <PointData>
+        <DataArray type="UInt64" Name="bulk_node_ids" format="appended" RangeMin="800"                  RangeMax="1111"                 offset="0"                   />
+      </PointData>
+      <CellData>
+        <DataArray type="UInt64" Name="bulk_element_ids" format="appended" RangeMin="735"                  RangeMax="1030"                 offset="344"                 />
+      </CellData>
+      <Points>
+        <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="appended" RangeMin="1.9999999289"         RangeMax="2.0000001344"         offset="676"                 />
+      </Points>
+      <Cells>
+        <DataArray type="Int64" Name="connectivity" format="appended" RangeMin=""                     RangeMax=""                     offset="1680"                />
+        <DataArray type="Int64" Name="offsets" format="appended" RangeMin=""                     RangeMax=""                     offset="2332"                />
+        <DataArray type="UInt8" Name="types" format="appended" RangeMin=""                     RangeMax=""                     offset="2664"                />
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+  <AppendedData encoding="base64">
+   _+AAAAAAAAAAgAwAAAAAAACEDAAAAAAAAIgMAAAAAAAAjAwAAAAAAACQDAAAAAAAAJQMAAAAAAAAmAwAAAAAAACcDAAAAAAAAKAMAAAAAAAApAwAAAAAAACoDAAAAAAAAKwMAAAAAAAAsAwAAAAAAAC0DAAAAAAAALgMAAAAAAAAvAwAAAAAAADEDAAAAAAAARgMAAAAAAABbAwAAAAAAAHADAAAAAAAAhQMAAAAAAACaAwAAAAAAAK8DAAAAAAAAxAMAAAAAAADZAwAAAAAAAO4DAAAAAAAAAwQAAAAAAAAYBAAAAAAAAC0EAAAAAAAAQgQAAAAAAABXBAAAAAAAAA==8AAAAAAAAADfAgAAAAAAAOACAAAAAAAA4QIAAAAAAADiAgAAAAAAAOMCAAAAAAAA5AIAAAAAAADlAgAAAAAAAOYCAAAAAAAA5wIAAAAAAADoAgAAAAAAAOkCAAAAAAAA6gIAAAAAAADrAgAAAAAAAOwCAAAAAAAA7QIAAAAAAADuAgAAAAAAAAIDAAAAAAAAFgMAAAAAAAAqAwAAAAAAAD4DAAAAAAAAUgMAAAAAAABmAwAAAAAAAHoDAAAAAAAAjgMAAAAAAACiAwAAAAAAALYDAAAAAAAAygMAAAAAAADeAwAAAAAAAPIDAAAAAAAABgQAAAAAAAA=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8AAAAAAAAAACAAAAAAAAAAQAAAAAAAAABgAAAAAAAAAIAAAAAAAAAAoAAAAAAAAADAAAAAAAAAAOAAAAAAAAABAAAAAAAAAAEgAAAAAAAAAUAAAAAAAAABYAAAAAAAAAGAAAAAAAAAAaAAAAAAAAABwAAAAAAAAAHgAAAAAAAAAgAAAAAAAAACIAAAAAAAAAJAAAAAAAAAAmAAAAAAAAACgAAAAAAAAAKgAAAAAAAAAsAAAAAAAAAC4AAAAAAAAAMAAAAAAAAAAyAAAAAAAAADQAAAAAAAAANgAAAAAAAAA4AAAAAAAAADoAAAAAAAAAPAAAAAAAAAA=HgAAAAAAAAADAwMDAwMDAwMDAwMDAwMDAwMDAwMDAwMDAwMDAwM=
+  </AppendedData>
+</VTKFile>

tools/ogs/test-data/quater_circle.vtu

@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32">
+  <UnstructuredGrid>
+    <Piece NumberOfPoints="31" NumberOfCells="30">
+      <PointData>
+        <DataArray type="UInt64" Name="bulk_node_ids" format="binary" RangeMin="800" RangeMax="1111">
+          +AAAACADAAAAAAAAIQMAAAAAAAAiAwAAAAAAACMDAAAAAAAAJAMAAAAAAAAlAwAAAAAAACYDAAAAAAAAJwMAAAAAAAAoAwAAAAAAACkDAAAAAAAAKgMAAAAAAAArAwAAAAAAACwDAAAAAAAALQMAAAAAAAAuAwAAAAAAAC8DAAAAAAAAMQMAAAAAAABGAwAAAAAAAFsDAAAAAAAAcAMAAAAAAACFAwAAAAAAAJoDAAAAAAAArwMAAAAAAADEAwAAAAAAANkDAAAAAAAA7gMAAAAAAAADBAAAAAAAABgEAAAAAAAALQQAAAAAAABCBAAAAAAAAFcEAAAAAAAA
+        </DataArray>
+      </PointData>
+      <CellData>
+        <DataArray type="UInt64" Name="bulk_element_ids" format="binary" RangeMin="735" RangeMax="1030">
+          8AAAAN8CAAAAAAAA4AIAAAAAAADhAgAAAAAAAOICAAAAAAAA4wIAAAAAAADkAgAAAAAAAOUCAAAAAAAA5gIAAAAAAADnAgAAAAAAAOgCAAAAAAAA6QIAAAAAAADqAgAAAAAAAOsCAAAAAAAA7AIAAAAAAADtAgAAAAAAAO4CAAAAAAAAAgMAAAAAAAAWAwAAAAAAACoDAAAAAAAAPgMAAAAAAABSAwAAAAAAAGYDAAAAAAAAegMAAAAAAACOAwAAAAAAAKIDAAAAAAAAtgMAAAAAAADKAwAAAAAAAN4DAAAAAAAA8gMAAAAAAAAGBAAAAAAAAA==
+        </DataArray>
+      </CellData>
+      <Points>
+        <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="1.9999999289" RangeMax="2.0000001344">
+          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
+        </DataArray>
+      </Points>
+      <Cells>
+        <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="30">
+          4AEAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIAAAAAAAAAAgAAAAAAAAADAAAAAAAAAAMAAAAAAAAABAAAAAAAAAAEAAAAAAAAAAUAAAAAAAAABQAAAAAAAAAGAAAAAAAAAAYAAAAAAAAABwAAAAAAAAAHAAAAAAAAAAgAAAAAAAAACAAAAAAAAAAJAAAAAAAAAAkAAAAAAAAACgAAAAAAAAAKAAAAAAAAAAsAAAAAAAAACwAAAAAAAAAMAAAAAAAAAAwAAAAAAAAADQAAAAAAAAANAAAAAAAAAA4AAAAAAAAADgAAAAAAAAAPAAAAAAAAAA8AAAAAAAAAEAAAAAAAAAAQAAAAAAAAABEAAAAAAAAAEQAAAAAAAAASAAAAAAAAABIAAAAAAAAAEwAAAAAAAAATAAAAAAAAABQAAAAAAAAAFAAAAAAAAAAVAAAAAAAAABUAAAAAAAAAFgAAAAAAAAAWAAAAAAAAABcAAAAAAAAAFwAAAAAAAAAYAAAAAAAAABgAAAAAAAAAGQAAAAAAAAAZAAAAAAAAABoAAAAAAAAAGgAAAAAAAAAbAAAAAAAAABsAAAAAAAAAHAAAAAAAAAAcAAAAAAAAAB0AAAAAAAAAHQAAAAAAAAAeAAAAAAAAAA==
+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="binary" RangeMin="2" RangeMax="60">
+          8AAAAAIAAAAAAAAABAAAAAAAAAAGAAAAAAAAAAgAAAAAAAAACgAAAAAAAAAMAAAAAAAAAA4AAAAAAAAAEAAAAAAAAAASAAAAAAAAABQAAAAAAAAAFgAAAAAAAAAYAAAAAAAAABoAAAAAAAAAHAAAAAAAAAAeAAAAAAAAACAAAAAAAAAAIgAAAAAAAAAkAAAAAAAAACYAAAAAAAAAKAAAAAAAAAAqAAAAAAAAACwAAAAAAAAALgAAAAAAAAAwAAAAAAAAADIAAAAAAAAANAAAAAAAAAA2AAAAAAAAADgAAAAAAAAAOgAAAAAAAAA8AAAAAAAAAA==
+        </DataArray>
+        <DataArray type="UInt8" Name="types" format="binary" RangeMin="3" RangeMax="3">
+          HgAAAAMDAwMDAwMDAwMDAwMDAwMDAwMDAwMDAwMDAwMDAw==
+        </DataArray>
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+</VTKFile>