diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
index a23c47a849941e089d81f1b8afccf26e4ef02b98..2ddc7bdd3c592727b08e59e5e0090cd473d42eb5 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
@@ -37,17 +37,17 @@ from linkahead.exceptions import (EmptyUniqueQueryError,
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
send_mail_with_defaults)
+from sample_helpers.utils import (CONSTANTS, get_column_header_name,
+ get_entity_name)
# suppress warning of diff function
-apilogger = logging.getLogger("caosdb.apiutils")
+apilogger = logging.getLogger("linkahead.apiutils")
apilogger.setLevel(logging.ERROR)
logger = logging.getLogger("caosadvancedtools")
-CACHE = {}
-
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
def cached_query(query, unique=False):
@@ -66,18 +66,20 @@ def reverse_semicolon_separated_list(value):
def generate_label_text(entity):
- if entity.get_property("Custom label") is not None and entity.get_property("Custom label").value:
- label = entity.get_property("Custom label").value
+ custom_label_prop_name = get_entity_name("custom_label_prop")
+ if entity.get_property(custom_label_prop_name) is not None and entity.get_property(custom_label_prop_name).value:
+ label = entity.get_property(custom_label_prop_name).value
else:
- label = entity.get_property("BIS label").value if entity.get_property(
- "BIS label") is not None else None
+ container_label_prop_name = get_entity_name("container_label_prop")
+ label = entity.get_property(container_label_prop_name).value if entity.get_property(
+ container_label_prop_name) is not None else None
if not label:
if not entity.name:
return entity.id
return f"{entity.id} {entity.name}"
if f"{label}" == f"{entity.id}":
- # prevent special case of BisLabel = BisID resulting in a preview
+ # prevent special case of Label = ID resulting in a preview
# that looks like "id, id".
return entity.id
return f"{entity.id} {label}"
@@ -85,7 +87,9 @@ def generate_label_text(entity):
def extract_parent_container(record, key):
- possible_parents = cached_query(f"FIND Container WHICH REFERENCES {record.id}")
+ possible_parents = cached_query(
+ f"FIND {get_entity_name('container_rt')} WHICH REFERENCES {record.id}"
+ )
values = []
for par in possible_parents:
@@ -103,9 +107,11 @@ def extract_bis_id(record, key):
def extract_custom_label(record, key):
- if record.get_property("Custom label") is not None:
+ custom_label_prop_name = get_entity_name("custom_label_prop")
+
+ if record.get_property(custom_label_prop_name) is not None:
- return record.get_property("Custom label").value
+ return record.get_property(custom_label_prop_name).value
return None
@@ -117,8 +123,9 @@ def extract_pi(record, key):
pi_id = record.get_property("PI").value
pi_rec = cached_query(f"FIND RECORD Person WITH ID={pi_id}", unique=True)
- if pi_rec.get_property("Abbreviation") is not None and pi_rec.get_property("Abbreviation").value is not None:
- return pi_rec.get_property("Abbreviation").value
+ abbr_prop_name = get_entity_name("abbreviation_prop")
+ if pi_rec.get_property(abbr_prop_name) is not None and pi_rec.get_property(abbr_prop_name).value is not None:
+ return pi_rec.get_property(abbr_prop_name).value
return pi_id
return None
@@ -145,11 +152,14 @@ def extract_collection(record, key):
def extract_container_type(record, key):
- if record.get_property("ContainerType") is not None and record.get_property("ContainerType").value is not None:
- ct_id = record.get_property("ContainerType").value
- ctr = cached_query(f"FIND ContainerType WITH ID={ct_id}", unique=True)
- if ctr.get_property("Abbreviation") is not None and ctr.get_property("Abbreviation").value is not None:
- return ctr.get_property("Abbreviation").value
+ abbr_prop_name = get_entity_name("abbreviation_prop")
+ containertype_rt_name = get_entity_name("containertype_rt")
+
+ if record.get_property(containertype_rt_name) is not None and record.get_property(containertype_rt_name).value is not None:
+ ct_id = record.get_property(containertype_rt_name).value
+ ctr = cached_query(f"FIND {containertype_rt_name} WITH ID={ct_id}", unique=True)
+ if ctr.get_property(abbr_prop_name) is not None and ctr.get_property(abbr_prop_name).value is not None:
+ return ctr.get_property(abbr_prop_name).value
return ct_id
return None
@@ -159,7 +169,7 @@ def extract_storage_chain(record, key):
def find_referencing_containers(eid):
containing_containers = []
- candidates = cached_query(f"FIND CONTAINER WHICH REFERENCES {eid}")
+ candidates = cached_query(f"FIND {get_entity_name('container_rt')} WHICH REFERENCES {eid}")
if len(candidates) > 1:
logger.debug(f"Entity {eid} is referenced by more than one container.")
return []
@@ -183,25 +193,25 @@ def default_extractor(record, key):
EXTRACTORS = {
- "BIS ID": extract_bis_id,
- "BIS label": default_extractor,
- "Collection": extract_collection,
- "Container Contents": default_extractor,
- "Container size": default_extractor,
- "Container type": extract_container_type,
- "Custom label": extract_custom_label,
- "PDFReport": default_extractor,
- "PI": extract_pi,
- "Parent container": extract_parent_container,
- "Storage chain": extract_storage_chain,
+ get_column_header_name("entity_id"): extract_bis_id,
+ get_column_header_name("container_label_prop"): default_extractor,
+ get_column_header_name("Collection"): extract_collection,
+ get_column_header_name("container_size_prop"): default_extractor,
+ get_column_header_name("containertype_rt"): extract_container_type,
+ get_column_header_name("custom_label_prop"): extract_custom_label,
+ get_column_header_name("PDFReport"): default_extractor,
+ get_column_header_name("PI"): extract_pi,
+ get_column_header_name("Parent container"): extract_parent_container,
+ get_column_header_name("Storage chain"): extract_storage_chain,
}
# List of sample properties to be ignored because they are treated
# otherwise. Similar, but not identical to SPECIAL TREATMENT.
IGNORE_KEYS = [
- "Child container", # To be changed by updating the child, not the parent.
- "ContainerType", # handled separately above
- "Responsible", # Not to be changed via upload
+ # To be changed by updating the child, not the parent.
+ get_column_header_name("child_container_prop"),
+ get_column_header_name("containertype_rt"), # handled separately above
+ get_column_header_name("Responsible"), # Not to be changed via upload
]
@@ -230,7 +240,7 @@ def retrieve_containers(data):
try:
container.append(
cached_query(
- f"FIND RECORD Container WITH id = '{bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{bis_id}'",
unique=True))
except EmptyUniqueQueryError as e:
# we want to warn about these
@@ -241,7 +251,8 @@ def retrieve_containers(data):
try:
container.append(
cached_query(
- f"FIND RECORD Container WITH id = '{next_bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{
+ next_bis_id}'",
unique=True))
found_at_least_one_in_range = True
except EmptyUniqueQueryError as e:
@@ -355,7 +366,7 @@ def main():
f"{ke}\n\nPlease contact your admin."
)
else:
- msg = "{}export_sample_csv.py was called without the JSON file in args.{}".format(
+ msg = "{} export_container_csv.py was called without the JSON file in args. {}".format(
ERROR_PREFIX, ERROR_SUFFIX)
logger.error(msg)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 729d795245c2b34e68e1b36d8b4cd47c1bb07d0b..ff0dd5afbad69e014f0f4e440660c43065d5a1d1 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -25,6 +25,7 @@ entity_names:
container_rt: Container
container_size_prop: "Container size"
containertype_rt: ContainerType
+ custom_label_prop: "Custom label"
labelcounter_prop: Counter
labelcounter_rt: LabelCounter
responsible_rt: Responsible