build triggered by submodule version

Author: openMINDS pipeline

openminds/collection.py

@@ -81,6 +81,13 @@ def save(self, path, individual_files=False, include_empty_properties=False):
 
         A list of the file paths created.
         """
+        # in case a user has added additional child nodes _after_ adding the parent node to the collection
+        # we first re-add all child nodes to the collection.
+        # This is probably not the most elegant or fast way to do this, but it is simple and robust.
+        for node in tuple(self.nodes.values()):
+            for linked_node in node.links:
+                self._add_node(linked_node)
+        # Now we can actually save the nodes
         if not individual_files:
             if os.path.exists(path):
                 if not os.path.isfile(path):

openminds/v3/chemicals/chemical_mixture.py

@@ -26,7 +26,7 @@ class ChemicalMixture(LinkedMetadata):
             formatting="text/markdown",
             multiline=True,
             description="Mention of what deserves additional attention or notice.",
-            instructions="Enter any additional remarks concerning this chemical mixture.",
+            instructions="Enter any additional remarks concering this chemical mixture.",
         ),
         Property(
             "has_part",

openminds/v3/chemicals/chemical_substance.py

@@ -26,7 +26,7 @@ class ChemicalSubstance(LinkedMetadata):
             formatting="text/markdown",
             multiline=True,
             description="Mention of what deserves additional attention or notice.",
-            instructions="Enter any additional remarks concerning this chemical substance.",
+            instructions="Enter any additional remarks concering this chemical substance.",
         ),
         Property(
             "lookup_label",

openminds/v3/controlled_terms/action_status_type.py

@@ -77,7 +77,7 @@ class ActionStatusType(LinkedMetadata):
             min_items=1,
             formatting="text/plain",
             description="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.",
-            instructions="Enter one or several synonyms (including abbreviations) for this controlled term.",
+            instructions="Enter one or several synonyms (inlcuding abbreviations) for this controlled term.",
         ),
     ]
 

openminds/v3/controlled_terms/age_category.py

@@ -77,7 +77,7 @@ class AgeCategory(LinkedMetadata):
             min_items=1,
             formatting="text/plain",
             description="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.",
-            instructions="Enter one or several synonyms (including abbreviations) for this controlled term.",
+            instructions="Enter one or several synonyms (inlcuding abbreviations) for this controlled term.",
         ),
     ]
 

openminds/v3/controlled_terms/analysis_technique.py

@@ -77,7 +77,7 @@ class AnalysisTechnique(LinkedMetadata):
             min_items=1,
             formatting="text/plain",
             description="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.",
-            instructions="Enter one or several synonyms (including abbreviations) for this controlled term.",
+            instructions="Enter one or several synonyms (inlcuding abbreviations) for this controlled term.",
         ),
     ]
 

openminds/v3/controlled_terms/anatomical_axes_orientation.py

@@ -77,7 +77,7 @@ class AnatomicalAxesOrientation(LinkedMetadata):
             min_items=1,
             formatting="text/plain",
             description="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.",
-            instructions="Enter one or several synonyms (including abbreviations) for this controlled term.",
+            instructions="Enter one or several synonyms (inlcuding abbreviations) for this controlled term.",
         ),
     ]
 

openminds/v3/controlled_terms/anatomical_identification_type.py

@@ -77,7 +77,7 @@ class AnatomicalIdentificationType(LinkedMetadata):
             min_items=1,
             formatting="text/plain",
             description="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.",
-            instructions="Enter one or several synonyms (including abbreviations) for this controlled term.",
+            instructions="Enter one or several synonyms (inlcuding abbreviations) for this controlled term.",
         ),
     ]
 

openminds/v3/controlled_terms/anatomical_plane.py

@@ -77,7 +77,7 @@ class AnatomicalPlane(LinkedMetadata):
             min_items=1,
             formatting="text/plain",
             description="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.",
-            instructions="Enter one or several synonyms (including abbreviations) for this controlled term.",
+            instructions="Enter one or several synonyms (inlcuding abbreviations) for this controlled term.",
         ),
     ]
 

openminds/v3/controlled_terms/annotation_criteria_type.py

@@ -77,7 +77,7 @@ class AnnotationCriteriaType(LinkedMetadata):
             min_items=1,
             formatting="text/plain",
             description="Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.",
-            instructions="Enter one or several synonyms (including abbreviations) for this controlled term.",
+            instructions="Enter one or several synonyms (inlcuding abbreviations) for this controlled term.",
         ),
     ]