Add support for openMINDS v4.0 (#32)

* Updated pipeline to support openMINDS v4.0 --------- Co-authored-by: openMINDS pipeline <[email protected]> Co-authored-by: Run tests by ehennestad <>
openMetadataInitiative · Nov 15, 2024 · 0f8aeb5 · 0f8aeb5
1 parent 6e17260
commit 0f8aeb5
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diff --git a/.github/badges/code_issues.svg b/.github/badges/code_issues.svg
diff --git a/code/+openminds/@Collection/Collection.m b/code/+openminds/@Collection/Collection.m
@@ -272,7 +272,7 @@ function updateLinks(obj)
                 obj openminds.Collection
                 savePath (1,1) string
                 options.SaveToSingleFile (1,1) logical = true
-                %options.IncludeEmptyProperties (1,1) logical = false
+                % options.IncludeEmptyProperties (1,1) logical = false
             end
 
             % Update links before saving
@@ -336,12 +336,11 @@ function load(obj, filePath)%, options)
         outputPaths = saveInstances(instance, filePath, options)
 
         instances = loadInstances(filePath)
-
     end
 
     methods (Access = protected)
 
-        %Add an instance to the Node container.
+        % Add an instance to the Node container.
         function addNode(obj, instance, options)
 
             arguments
@@ -362,7 +361,7 @@ function addNode(obj, instance, options)
 
             if isConfigured(obj.Nodes)
                 if isKey(obj.Nodes, instance.id)
-                    %warning('Node with id %s already exists in collection', instance.id)
+                    % warning('Node with id %s already exists in collection', instance.id)
                     if options.AbortIfNodeExists
                         return
                     end
@@ -389,7 +388,7 @@ function addNode(obj, instance, options)
             obj.addSubNodes(instance)
         end
 
-        %Add sub node instances (linked types) to the Node container.
+        % Add sub node instances (linked types) to the Node container.
         function addSubNodes(obj, instance)
             % Add links.
             linkedTypes = instance.getLinkedTypes();

diff --git a/code/+openminds/@Collection/loadInstances.m b/code/+openminds/@Collection/loadInstances.m
@@ -9,7 +9,7 @@
 
     arguments
         filePath (1,:) string = ""
-        %options.RecursionDepth = 1
+        % options.RecursionDepth = 1
     end
 
     import openminds.internal.serializer.JsonLdSerializer
@@ -39,7 +39,7 @@
 
                 if ~isfield(thisInstance, 'at_type')
                     continue % Todo: Why skip?
-                    %instances{i} = struct('id', thisInstance.at_id);
+                    % instances{i} = struct('id', thisInstance.at_id);
                 else
                     openMindsType = thisInstance.at_type;
                     className = openminds.internal.utility.string.type2class(openMindsType);

diff --git a/code/enumerations/latest/+openminds/+enum/Models.m b/code/enumerations/latest/+openminds/+enum/Models.m
@@ -1,12 +1,12 @@
 classdef Models
     enumeration
+        SANDS
+        chemicals
         computation
-        publications
         controlledTerms
-        chemicals
-        SANDS
         core
         ephys
+        publications
         specimenPrep
         stimulation
     end

diff --git a/code/enumerations/latest/+openminds/+enum/Types.m b/code/enumerations/latest/+openminds/+enum/Types.m
@@ -1,5 +1,4 @@
 classdef Types < openminds.abstract.TypesEnumeration
-
     enumeration
         None('None')
         AtlasAnnotation("openminds.sands.atlas.AtlasAnnotation")
@@ -221,5 +220,4 @@
         StimulationActivity("openminds.stimulation.activity.StimulationActivity")
         EphysStimulus("openminds.stimulation.stimulus.EphysStimulus")
     end
-
 end
diff --git a/code/enumerations/v1.0/+openminds/+enum/Types.m b/code/enumerations/v1.0/+openminds/+enum/Types.m
@@ -1,5 +1,4 @@
 classdef Types < openminds.abstract.TypesEnumeration
-
     enumeration
         None('None')
         AnatomicalEntity("openminds.sands.AnatomicalEntity")
@@ -88,5 +87,4 @@
         TissueSampleCollectionState("openminds.core.research.TissueSampleCollectionState")
         TissueSampleState("openminds.core.research.TissueSampleState")
     end
-
 end
diff --git a/code/enumerations/v2.0/+openminds/+enum/Types.m b/code/enumerations/v2.0/+openminds/+enum/Types.m
@@ -1,5 +1,4 @@
 classdef Types < openminds.abstract.TypesEnumeration
-
     enumeration
         None('None')
         AtlasAnnotation("openminds.sands.atlas.AtlasAnnotation")
@@ -102,5 +101,4 @@
         TissueSampleCollectionState("openminds.core.research.TissueSampleCollectionState")
         TissueSampleState("openminds.core.research.TissueSampleState")
     end
-
 end
diff --git a/code/enumerations/v3.0/+openminds/+enum/Models.m b/code/enumerations/v3.0/+openminds/+enum/Models.m
@@ -1,12 +1,12 @@
 classdef Models
     enumeration
+        SANDS
+        chemicals
         computation
-        publications
         controlledTerms
-        chemicals
-        SANDS
         core
         ephys
+        publications
         specimenPrep
         stimulation
     end

diff --git a/code/enumerations/v3.0/+openminds/+enum/Types.m b/code/enumerations/v3.0/+openminds/+enum/Types.m
@@ -1,5 +1,4 @@
 classdef Types < openminds.abstract.TypesEnumeration
-
     enumeration
         None('None')
         AtlasAnnotation("openminds.sands.atlas.AtlasAnnotation")
@@ -219,5 +218,4 @@
         StimulationActivity("openminds.stimulation.activity.StimulationActivity")
         EphysStimulus("openminds.stimulation.stimulus.EphysStimulus")
     end
-
 end
diff --git a/code/enumerations/v4.0/+openminds/+enum/Models.m b/code/enumerations/v4.0/+openminds/+enum/Models.m
@@ -0,0 +1,13 @@
+classdef Models
+    enumeration
+        SANDS
+        chemicals
+        computation
+        controlledTerms
+        core
+        ephys
+        publications
+        specimenPrep
+        stimulation
+    end
+end