using readonly instead of user_editability; enabling injesting multip…

src/pynxtools/nomad/parser.py

@@ -513,7 +513,7 @@ def parse(
         if archive.metadata.entry_type is None:
             archive.metadata.entry_type = app_def
             archive.metadata.domain = "nexus"
-        archive.metadata.user_editable = False
+        archive.metadata.readonly = True
 
         # Normalise element info
         if archive.results is None:

src/pynxtools/nomad/schema.py

@@ -47,6 +47,7 @@
         InstrumentReference,
         Measurement,
     )
+    from nomad.datamodel.metainfo.workflow import Link, Task, Workflow
     from nomad.metainfo import (
         Attribute,
         Bytes,
@@ -105,8 +106,8 @@
     "NXsample": [CompositeSystem],
     "NXsample_component": [Component],
     "NXidentifier": [EntityReference],
-    "NXentry": [ActivityStep],
-    "NXprocess": [ActivityStep],
+    "NXentry": [ActivityStep],  # , Task],
+    "NXprocess": [ActivityStep],  # , Task],
     "NXdata": [ActivityResult],
     # "object": BaseSection,
 }
@@ -139,7 +140,44 @@ def normalize(self, archive, logger):
                 self.method = self.m_def.name + " Experiment"
         except (AttributeError, TypeError):
             pass
-        super(NexusMeasurement, self).normalize(archive, logger)
+        super(basesections.Activity, self).normalize(archive, logger)
+
+        if archive.results.eln.methods is None:
+            archive.results.eln.methods = []
+        if self.method:
+            archive.results.eln.methods.append(self.method)
+        else:
+            archive.results.eln.methods.append(self.m_def.name)
+        if archive.workflow2 is None:
+            archive.workflow2 = Workflow(name=self.name)
+        # steps to tasks
+        act_array = archive.workflow2.tasks
+        existing_items = {(task.name, task.section) for task in act_array}
+        new_items = [
+            item.to_task()
+            for item in self.steps
+            if (item.name, item) not in existing_items
+        ]
+        act_array.extend(new_items)
+        # samples to inputs
+        act_array = archive.workflow2.inputs
+        existing_items = {(link.name, link.section) for link in act_array}
+        new_items = [
+            Link(name=item.name, section=item.reference)
+            for item in self.samples
+            if (item.name, item.reference) not in existing_items
+        ]
+        act_array.extend(new_items)
+
+        # results to outputs
+        act_array = archive.workflow2.outputs
+        existing_items = {(link.name, link.section) for link in act_array}
+        new_items = [
+            Link(name=item.name, section=item)
+            for item in self.results
+            if (item.name, item) not in existing_items
+        ]
+        act_array.extend(new_items)
 
 
 VALIDATE = False
@@ -952,7 +990,7 @@ def normalize_sample(self, archive, logger):
     """Normalizer for sample section."""
     current_cls = __section_definitions[__rename_nx_for_nomad("NXsample")].section_cls
     self.name = self.__dict__["nx_name"] + (
-        "(" + self.name__field + ")" if self.name__field else ""
+        " (" + self.name__field + ")" if self.name__field else ""
     )
     # one could also copy local ids to identifier for search purposes
     super(current_cls, self).normalize(archive, logger)
@@ -964,12 +1002,18 @@ def normalize_entry(self, archive, logger):
     if self.start_time__field:
         self.start_time = self.start_time__field
     self.name = self.__dict__["nx_name"] + (
-        "(" + self.title__field + ")" if self.title__field is not None else ""
+        " (" + self.title__field + ")" if self.title__field is not None else ""
     )
     # one could also copy local ids to identifier for search purposes
     super(current_cls, self).normalize(archive, logger)
 
 
+# def to_task_itself(self):
+#     """takes advantage if an object itself is also a Task"""
+#     self.section=self
+#     return self
+
+
 def normalize_process(self, archive, logger):
     """Normalizer for Process section."""
     current_cls = __section_definitions[__rename_nx_for_nomad("NXprocess")].section_cls
@@ -998,7 +1042,7 @@ def create_Entity(lab_id, archive, f_name):
             data=entitySec,
             m_context=archive.m_context,
             metadata=EntryMetadata(
-                entry_type="identifier", domain="nexus"
+                entry_type="identifier", domain="nexus", readonly=True
             ),  # upload_id=archive.m_context.upload_id,
         )
         with archive.m_context.raw_file(f_name, "w") as f_obj:
@@ -1039,8 +1083,14 @@ def get_entry_reference(archive, f_name):
     __rename_nx_for_nomad("NXsample"): normalize_sample,
     __rename_nx_for_nomad("NXsample_component"): normalize_sample_component,
     __rename_nx_for_nomad("NXidentifier"): normalize_identifier,
-    __rename_nx_for_nomad("NXentry"): normalize_entry,
-    __rename_nx_for_nomad("NXprocess"): normalize_process,
+    __rename_nx_for_nomad("NXentry"): {
+        "normalize": normalize_entry,
+        # "to_task": to_task_itself,
+    },
+    __rename_nx_for_nomad("NXprocess"): {
+        "normalize": normalize_process,
+        # "to_task": to_task_itself,
+    },
     __rename_nx_for_nomad("NXdata"): normalize_data,
 }
 
@@ -1053,4 +1103,8 @@ def get_entry_reference(archive, f_name):
 
     # Append the normalize method from a function
     if normalize_func:
-        section.section_cls.normalize = normalize_func
+        if isinstance(normalize_func, dict):
+            for key, value in normalize_func.items():
+                setattr(section.section_cls, key, value)
+        else:
+            section.section_cls.normalize = normalize_func