diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index 985a5d130ab3bce50e10c0d9820c610372d2b2b3..4739d5c4ea22ac6a613afbf468285d21e80d1fc8 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -211,64 +211,60 @@ def main():
logger.warning(f"There is no PI with ID or {get_entity_name('abbreviation_prop')} {pi}. Skipping.")
# Collection(s)
- if _value_in_row("Collection", row):
- collection_rt = cached_get_entity_by(query="FIND RECORDTYPE Collection")
- if not ";" in str(row["Collection"]):
- collections = [row["Collection"]]
+ if _value_in_row(get_column_header_name("Collection"), row):
+ collection_rt = cached_get_entity_by(query=f"FIND RECORDTYPE '{get_entity_name('Collection')}'")
+ if not ";" in str(row[get_column_header_name("Collection")]):
+ collections = [row[get_column_header_name("Collection")]]
else:
- collections = [coll.strip() for coll in str(row["Collection"]).split(';')]
+ collections = [coll.strip() for coll in str(row[get_column_header_name("Collection")]).split(';')]
prop_val = []
for coll in collections:
try:
- query = f"FIND RECORD Collection WITH ID={int(coll)}"
+ query = f"FIND '{collection_rt.name}' WITH ID={int(coll)}"
except ValueError:
- query = f"FIND RECORD Collection WITH name='{coll}'"
+ query = f"FIND RECORD '{collection_rt.name}' WITH name='{coll}'"
try:
coll_rec = cached_get_entity_by(query=query)
prop_val.append(coll_rec.id)
except db.EmptyUniqueQueryError:
- logger.warning(f"There is no collection with name or BIS ID {coll}. Skipping.")
+ logger.warning(f"There is no {collection_rt.name} with name or ID {coll}. Skipping.")
continue
if prop_val:
- if child.get_property("Collection") is not None:
- child.get_property("Collection").datatype = db.LIST("Collection")
- child.get_property("Collection").value = prop_val
+ if child.get_property(collection_rt.name) is not None:
+ child.get_property(collection_rt.name).datatype = db.LIST(collection_rt.name)
+ child.get_property(collection_rt.name).value = prop_val
else:
child.add_property(id=collection_rt.id, name=collection_rt.name, datatype=db.LIST(
- "Collection"), value=prop_val)
+ collection_rt.name), value=prop_val)
# Treat Container Contents
- if _value_in_row("Container Contents", row):
- if not (_value_in_row("PI", row) and _value_in_row("Collection", row)):
- logger.error(
- f"Container Contents are given for container {child.id} but it "
- "is missing PI and/or Collection info. No updates have been performed."
- )
- return 1
- contents_prop = cached_get_entity_by(query="FIND PROPERTY 'Container Contents'")
+ if _value_in_row(get_column_header_name("Container Contents"), row):
+ contents_prop = cached_get_entity_by(
+ query=f"FIND PROPERTY '{get_entity_name('Container Contents')}'"
+ )
if child.get_property(contents_prop.name) is not None:
- child.get_property(contents_prop.name).value = row["Container Contents"]
+ child.get_property(contents_prop.name).value = row[get_column_header_name("Container Contents")]
else:
child.add_property(id=contents_prop.id, name=contents_prop.name,
- value=row["Container Contents"])
+ value=row[get_column_header_name("Container Contents")])
# Treat PDF Report
- if _value_in_row("PDFReport", row):
- pdf_id = row["PDFReport"]
+ if _value_in_row(get_column_header_name("PDFReport"), row):
+ pdf_id = row[get_column_header_name("PDFReport")]
try:
pdf_id = int(pdf_id)
- pdf_rec = cached_query(f"FIND FILE PDFReport WITH ID={pdf_id}")
+ pdf_rec = cached_query(f"FIND FILE {get_entity_name('PDFReport')} WITH ID={pdf_id}")
if not pdf_rec:
logger.warning(
- f"There is no PDFReport with Bis ID {pdf_id}, so no PDF is attached to container {child.id}.")
+ f"There is no PDFReport with ID {pdf_id}, so no PDF is attached to container {child.id}.")
else:
- if child.get_property("PDFReport") is not None:
- child.get_property("PDFReport").value = pdf_id
+ if child.get_property(get_entity_name("PDFReport")) is not None:
+ child.get_property(get_property("PDFReport")).value = pdf_id
else:
child.add_property(id=pdf_rt.id, name=pdf_rt.name, value=pdf_id)
except ValueError:
logger.warning(
- f"There is no valid Bis ID provided for container {child.id}."
+ f"There is no valid ID provided for container {child.id}."
f"Provided was {pdf_id}. Skipping")
# This is a workaround for weird merging errors in the
@@ -276,13 +272,13 @@ def main():
# following release.
merged = []
for par in parent_containers:
- if (data['BIS ID'] == par.id).any():
+ if (data[id_column_name] == par.id).any():
# A container to be updated is used as another containers parent:
child = child_containers.get_entity_by_id(par.id)
# All parents have a child sample property with a value (which may
# be empty). No child sample has this property, so the following is
# okay without checks:
- prop = par.get_property("Child container")
+ prop = par.get_property(child_container_prop.name)
child.add_property(name=prop.name, id=prop.id, value=prop.value)
merged.append(par)
for par in merged: