FIX: Fix typos and datamodel problems

models_and_helper_scripts/sample-management-datamodel.yml

@@ -65,10 +65,10 @@ Container:
   obligatory_properties:
     Responsible:
     ContainerType:
+  suggested_properties:
     container_label:
       description: A standardized label for a container
       datatype: TEXT
-  suggested_properties:
     Child container:
       datatype: LIST<Container>
     Container size:

sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py

@@ -28,7 +28,7 @@ import json
 import logging
 import sys
 
-import caosdb as db
+import linkahead as db
 from caosadvancedtools.serverside import helper
 from caosadvancedtools.serverside.logging import configure_server_side_logging
 
@@ -126,16 +126,18 @@ def create_container_entities(responsible_id, container_type_id, container_size,
     # Post process child containers
     batch = post_process_containers(batch)
     try:
+        logger.info(batch)
         batch.insert()
-    except:
-        logger.error("{}The registered containers could not be imported to the system.{}".format(
+    except Exception as e:
+        logger.error("{} The registered containers could not be imported to the system. {}".format(
             ERROR_PREFIX, ERROR_SUFFIX))
+        logger.error(e)
         return None
         # TODO: Reset the internal_container_label_counter of person to its previous value if nothing has be inserted
 
     # Add to parent container
     if parent_container is not None:
-        child_cont_prop = db.Property(name=get_entity_name("child_container_prop").retrieve()
+        child_cont_prop = db.Property(name=get_entity_name("child_container_prop")).retrieve()
         new_childs=[]
         for entity in batch:
             new_childs += [entity.id]
@@ -148,7 +150,7 @@ def create_container_entities(responsible_id, container_type_id, container_size,
                 parent_container.get_property(child_cont_prop.name).value=new_childs
             else:
                 parent_container.get_property(child_cont_prop.name).value += new_childs
-        parent_container=post_process_parent_container(parent)
+        parent_container=post_process_parent_container(parent_container)
         parent_container.update()
 
     set_label_counter(container_type_id=container_type_id,

sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py

@@ -55,8 +55,8 @@ def get_container_name_prefix(responsible_id: int, container_type_id: int) -> st
         Name in the format `<responsible>_<container_type_name>`
 
     """
-    resp = db.cached_get_entity_by(eid=responsible_id)
-    ct = db.cached_get_entity_by(eid=container_type_id)
+    resp = db.cached.cached_get_entity_by(eid=responsible_id)
+    ct = db.cached.cached_get_entity_by(eid=container_type_id)
 
     resp_str = get_record_string(resp)
     ct_str = get_record_string(ct)

sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py

@@ -3,10 +3,12 @@ import yaml
 
 from pathlib import Path
 
-CONSTANTS = yaml.load(os.path.join(Path(__file__).parent, "default_constants.yml"))
+with open(os.path.join(Path(__file__).parent, "default_constants.yml")) as yaml_file:
+    CONSTANTS = yaml.safe_load(yaml_file)
 
 if os.path.isfile(os.path.join(Path(__file__).parent, "constants.yml")):
-    CONSTANTS.update(yaml.load(os.path.join(Path(__file__).parent, "constants.yml")))
+    with open(os.path.join(Path(__file__).parent, "constants.yml")) as custom_yaml_file:
+        CONSTANTS.update(yaml.safe_load(custom_yaml_file))
 
 
 def get_entity_name(name: str):
@@ -21,6 +23,6 @@ def get_entity_name(name: str):
 def get_column_header_name(name: str):
 
     if name in CONSTANTS["csv_column_names"]:
-        return CONSTANTS["csv_column_names"]
+        return CONSTANTS["csv_column_names"][name]
 
     return get_entity_name(name)