add curated annotation and small fixes

bluepyemodel/access_point/forge_access_point.py

@@ -351,7 +351,6 @@ def add_images_to_resource(self, images, resource, filters_existence=None):
                 can be used to search for existence of resource on nexus.
                 Used to get image type if cannot be extracted from image path.
         """
-        resource = Dataset.from_resource(self.forge, resource, store_metadata=True)
         if filters_existence is None:
             filters_existence = {}
         for path in images:
@@ -426,8 +425,12 @@ def register(
         resource = self.forge.from_json(resource_description, na="None")
         resource = self.add_contribution(resource)
 
-        if distributions:
+        if distributions or images:
+            # do this before adding lazy actions.
+            # if we do it after, it turns the lazy actions into a str
             resource = Dataset.from_resource(self.forge, resource)
+
+        if distributions:
             for path in distributions:
                 resource.add_distribution(path, content_type=f"application/{path.split('.')[-1]}")
 

bluepyemodel/access_point/nexus.py

@@ -286,12 +286,19 @@ def get_nexus_subject(self, species):
         return subject
 
     def store_object(
-        self, object_, seed=None, description=None, currents=None, is_analysis_suitable=False
+        self,
+        object_,
+        seed=None,
+        description=None,
+        currents=None,
+        is_analysis_suitable=False,
+        is_curated=False,
     ):
         """Store a BPEM object on Nexus"""
 
         metadata_dict = self.emodel_metadata_ontology.for_resource(
-            is_analysis_suitable=is_analysis_suitable
+            is_analysis_suitable=is_analysis_suitable,
+            is_curated=is_curated,
         )
         if seed is not None:
             metadata_dict["seed"] = seed
@@ -622,11 +629,15 @@ def create_emodel_workflow(self, state="not launched"):
         except AccessPointException:
             targets_configuration_id = None
 
-        pipeline_settings_id = self.access_point.get_nexus_id(
-            type_="EModelPipelineSettings",
-            metadata=self.emodel_metadata_ontology.filters_for_resource(),
-            legacy_metadata=self.emodel_metadata_ontology.filters_for_resource_legacy(),
-        )
+        try:
+            pipeline_settings_id = self.access_point.get_nexus_id(
+                type_="EModelPipelineSettings",
+                metadata=self.emodel_metadata_ontology.filters_for_resource(),
+                legacy_metadata=self.emodel_metadata_ontology.filters_for_resource_legacy(),
+            )
+        except AccessPointException:
+            pipeline_settings_id = None
+
         emodel_configuration_id = self.access_point.get_nexus_id(
             type_="EModelConfiguration",
             metadata=self.emodel_metadata_ontology.filters_for_resource(),
@@ -803,6 +814,7 @@ def store_emodel(self, emodel, description=None):
             )
 
         emodel.workflow_id = nexus_id
+        # make it analysis suitable AND curated if this is True
         is_analysis_suitable = (
             self.has_fitness_calculator_configuration
             and self.has_model_configuration
@@ -814,6 +826,7 @@ def store_emodel(self, emodel, description=None):
             seed=emodel.seed,
             description=description,
             is_analysis_suitable=is_analysis_suitable,
+            is_curated=is_analysis_suitable,
         )
         # wait for the object to be uploaded and fetchable
         time.sleep(self.sleep_time)

bluepyemodel/emodel_pipeline/emodel_metadata.py

@@ -126,7 +126,7 @@ def ttype_annotation_dict(self):
             "name": "T-type annotation",
         }
 
-    def annotation_list(self, is_analysis_suitable=False):
+    def annotation_list(self, is_analysis_suitable=False, is_curated=False):
         """Returns an annotation list containing mtype, etype and ttype annotations.
 
         Args:
@@ -148,6 +148,19 @@ def annotation_list(self, is_analysis_suitable=False):
                     "note": "Analysis can be run on this model.",
                 }
             )
+        if is_curated:
+            annotation_list.append(
+                {
+                    "@type": ["QualityAnnotation", "Annotation"],
+                    "hasBody": {
+                        "@id": "https://neuroshapes.org/Curated",
+                        "@type": ["AnnotationBody", "DataMaturity"],
+                        "label": "Curated",
+                    },
+                    "motivatedBy": {"@id": "quality:Assessment", "@type": "Motivation"},
+                    "name": "Data maturity annotation",
+                }
+            )
         if self.etype:
             annotation_list.append(self.etype_annotation_dict())
         if self.mtype:
@@ -201,7 +214,7 @@ def filters_for_resource_legacy(self):
         """Legacy metadata used for filtering, without the annotation list"""
         return self.as_dict_for_resource_legacy()
 
-    def for_resource(self, is_analysis_suitable=False):
+    def for_resource(self, is_analysis_suitable=False, is_curated=False):
         """Metadata to add to a resource to register.
 
         DO NOT use for filtering. For filtering, use self.filters_for_resource() instead.
@@ -213,7 +226,9 @@ def for_resource(self, is_analysis_suitable=False):
 
         metadata = self.as_dict_for_resource()
 
-        metadata["annotation"] = self.annotation_list(is_analysis_suitable=is_analysis_suitable)
+        metadata["annotation"] = self.annotation_list(
+            is_analysis_suitable=is_analysis_suitable, is_curated=is_curated
+        )
 
         return metadata