From 9f0b992d9056cb3dc8bc6de007875616d1894828 Mon Sep 17 00:00:00 2001
From: sanbrock <sandor.brockhauser@gmail.com>
Date: Wed, 18 Dec 2024 13:37:54 +0100
Subject: [PATCH] moving changes to NeXusMeasurement which is not anymore using
 normalisation from Measurement and Activity

---
 src/pynxtools/nomad/schema.py | 56 +++++++++++++++++++++++++++++------
 1 file changed, 47 insertions(+), 9 deletions(-)

diff --git a/src/pynxtools/nomad/schema.py b/src/pynxtools/nomad/schema.py
index 81846327c..81bc40f8b 100644
--- a/src/pynxtools/nomad/schema.py
+++ b/src/pynxtools/nomad/schema.py
@@ -106,8 +106,8 @@
     "NXsample": [CompositeSystem],
     "NXsample_component": [Component],
     "NXidentifier": [EntityReference],
-    "NXentry": [ActivityStep, Task],
-    "NXprocess": [ActivityStep, Task],
+    "NXentry": [ActivityStep],  # , Task],
+    "NXprocess": [ActivityStep],  # , Task],
     "NXdata": [ActivityResult],
     # "object": BaseSection,
 }
@@ -140,7 +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(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
@@ -971,9 +1008,10 @@ def normalize_entry(self, archive, logger):
     super(current_cls, self).normalize(archive, logger)
 
 
-def to_task_itself(self):
-    """takes advantage if an object itself is also a Task"""
-    return self
+# 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):
@@ -1004,7 +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:
@@ -1047,11 +1085,11 @@ def get_entry_reference(archive, f_name):
     __rename_nx_for_nomad("NXidentifier"): normalize_identifier,
     __rename_nx_for_nomad("NXentry"): {
         "normalize": normalize_entry,
-        "to_task": to_task_itself,
+        # "to_task": to_task_itself,
     },
     __rename_nx_for_nomad("NXprocess"): {
         "normalize": normalize_process,
-        "to_task": to_task_itself,
+        # "to_task": to_task_itself,
     },
     __rename_nx_for_nomad("NXdata"): normalize_data,
 }