MAINT: Remove bis from container id variable in web form

sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js

@@ -6,12 +6,12 @@
 'use strict';
 
 /**
- * @module ext_bis_stockmanagement
+ * @module ext_stockmanagement
  * @version 0.2
  *
  * @requires($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver)
  */
-const ext_bis_stockmanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
+const ext_stockmanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
 
     const tool_box = "Storage Management" // The item that is shown in the top-navbar
 
@@ -115,7 +115,7 @@ const ext_bis_stockmanagement = function($, navbar, log, form_elements, form_pan
         script: "export_container_csv.py",
         fields: [{
             type: "text",
-            name: "bis_ids",
+            name: "container_ids",
             label: container_id_label,
             required: true,
             pattern: "((([0-9]+\\s*-\\s*){0,1}[0-9]+)\\s*,\\s*)*(([0-9]+\\s*-\\s*){0,1}[0-9]+)",

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

@@ -100,7 +100,7 @@ def extract_parent_container(record, key):
     return reverse_semicolon_separated_list(values)
 
 
-def extract_bis_id(record, key):
+def extract_eid(record, key):
 
     return record.id
 
@@ -193,7 +193,7 @@ def default_extractor(record, key):
 
 
 EXTRACTORS = {
-    get_column_header_name("entity_id"): extract_bis_id,
+    get_column_header_name("entity_id"): extract_eid,
     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,
@@ -235,29 +235,29 @@ def retrieve_containers(data):
 
     container = []
     not_found = []
-    for bis_id in data:
-        if isinstance(bis_id, int):
+    for eid in data:
+        if isinstance(eid, int):
             try:
                 container.append(
                     cached_query(
-                        f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{bis_id}'",
+                        f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{eid}'",
                         unique=True))
             except EmptyUniqueQueryError as e:
                 # we want to warn about these
-                not_found.append(bis_id)
+                not_found.append(eid)
         else:
             found_at_least_one_in_range = False
-            for next_bis_id in bis_id:
+            for next_eid in eid:
                 try:
                     container.append(
                         cached_query(
-                            f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{next_bis_id}'",
+                            f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{next_eid}'",
                             unique=True))
                     found_at_least_one_in_range = True
                 except EmptyUniqueQueryError as e:
                     pass
             if not found_at_least_one_in_range:
-                not_found.append(f"{bis_id.start}-{bis_id.stop-1}")
+                not_found.append(f"{eid.start}-{eid.stop-1}")
     return container, not_found
 
 
@@ -325,7 +325,7 @@ def main():
         with open(args.filename) as form_json:
             form_data = json.load(form_json)
 
-            tmp = form_data["bis_ids"].split(",")
+            tmp = form_data["container_ids"].split(",")
             data = []
             for d in tmp:
                 if "-" in d:

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

@@ -37,7 +37,7 @@ from linkahead.cached import cached_query, cached_get_entity_by
 from bis_utils import (get_do_not_insert_type_names,
                        replace_entity_urls_by_ids, whitespace_cleanup_in_df)
 from sample_helpers.container_update_get_parent import get_container_by_identifier
-from sample_helpers.utils import CONSTANTS
+from sample_helpers.utils import (CONSTANTS, get_column_header_name, get_entity_name)
 
 # suppress warning of diff function
 apilogger = logging.getLogger("linkahead.apiutils")
@@ -89,29 +89,35 @@ def main():
     # Get referenced container entities
     child_containers = db.Container()
     parent_containers = db.Container()
+    id_column_name = get_column_header_name("entity_id")
+    parent_column_name = get_column_header_name("Parent container")
     for index, row in data.iterrows():
-        if not _value_in_row("BIS ID", row):
-            logger.error(f"BIS ID is missing in row {index+1}. Nothing was updated.")
+        if not _value_in_row(id_column_name, row):
+            logger.error(f"{id_column_name} is missing in row {index+1}. Nothing was updated.")
             return 1
         try:
-            child = db.Record(id=int(row["BIS ID"]))
+            child = db.Record(id=int(row[id_column_name]))
         except ValueError:
             logger.error(
-                f"Invalid BIS ID {row['BIS ID']} in row {index + 1}. Nothing was updated.")
+                f"Invalid {id_column_name} {row[id_column_name]} in row {index + 1}. Nothing was updated.")
             return 1
-        child.add_parent("Container")
+        child.add_parent(get_entity_name("container_rt"))
         child_containers.append(child)
         
-        if _value_in_row("Parent container", row):
-            parent_identifier = row["Parent container"]
+        if _value_in_row(parent_column_name, row):
+            parent_identifier = row[parent_column_name]
             parent = get_container_by_identifier(parent_identifier)
             if len(parent) == 0:
                 logger.error(
-                    f"Couldn't find parent with identifier '{parent_identifier}' in row {index+1}.")
+                    f"Couldn't find parent with identifier '{parent_identifier}' "
+                    f"in row {index+1}."
+                )
                 return 1
             elif len(parent) > 1:
-                logger.error(f"Parent with identifier '{parent_identifier}' in row {index+1} was not unique. "
-                             "Please specify with BIS ID instead.")
+                logger.error(
+                    f"Parent with identifier '{parent_identifier}' in row "
+                    f"{index+1} was not unique. Please specify with "
+                    f"{id_column_name} instead.")
                 return 1
             parent = parent[0]
             try:
@@ -125,16 +131,22 @@ def main():
         return 1
 
     # Get IDs of proerperties
-    child_container_prop = cached_get_entity_by(query="FIND Property WITH name = 'Child container'")
-    custom_label_prop = cached_get_entity_by(query="FIND Property WITH name = 'Custom label'")
-    pdf_rt = cached_get_entity_by(query="FIND RECORDTYPE WITH name=PDFReport")
+    child_container_prop = cached_get_entity_by(
+        query=f"FIND Property WITH name = '{get_entity_name('child_container_prop')}'"
+    )
+    custom_label_prop = cached_get_entity_by(
+        query=f"FIND Property WITH name = '{get_entity_name('custom_label_prop')}'"
+    )
+    pdf_rt = cached_get_entity_by(
+        query=f"FIND RECORDTYPE WITH name='{get_entity_name('PDFReport')}'"
+    )
 
     # Update (/create) container entities
     for index, row in data.iterrows():
         # Add child to parent
         parent = None
-        if _value_in_row("Parent container", row):
-            parent_identifier = row["Parent container"]
+        if _value_in_row(parent_column_name, row):
+            parent_identifier = row[parent_column_name]
             # This has already been checked above for uniqueness
             candidate = get_container_by_identifier(parent_identifier)[0]
             # A bit redundant, but we need the exact Python object here that is in the parent_containers list.
@@ -142,17 +154,21 @@ def main():
 
             if parent.get_property(child_container_prop.id) is None:
                 parent.add_property(id=child_container_prop.id,
-                                    name=child_container_prop.name, value=[int(row["BIS ID"])])
+                                    name=child_container_prop.name, value=[int(row[id_column_name])])
             else:
                 if parent.get_property(child_container_prop.id).value is None:
-                    parent.get_property(child_container_prop.id).value = [int(row["BIS ID"])]
+                    parent.get_property(child_container_prop.id).value = [int(row[id_column_name])]
                 else:
-                    if int(row["BIS ID"]) not in parent.get_property(child_container_prop.id).value:
+                    if int(row[id_column_name]) not in parent.get_property(child_container_prop.id).value:
                         parent.get_property(child_container_prop.id).value.append(
-                            int(row["BIS ID"]))
+                            int(row[id_column_name]))
 
-            # remove the current child from all other parents (don't do anything if the parent didn't change)
-            old_parents = cached_query(f"FIND Container WHICH REFERENCES {int(row['BIS ID'])}")
+            # remove the current child from all other parents (don't
+            # do anything if the parent didn't change)
+            old_parents = cached_query(
+                f"FIND {get_entity_name('container_rt')} WHICH REFERENCES "
+                f"{int(row[id_column_name])}"
+            )
             for old_parent in old_parents:
                 if parent is not None and old_parent.id == parent.id:
                     # old parent also is new parent
@@ -162,20 +178,20 @@ def main():
                     old_parent = parent_containers.get_entity_by_id(old_parent.id)
                 except KeyError:
                     parent_containers.append(old_parent)
-                old_parent.remove_value_from_property("Child container", int(
-                    row["BIS ID"]), remove_if_empty_afterwards=False)
-                if old_parent.get_property("Child container").value is None:
-                    old_parent.get_property("Child container").value = []
+                old_parent.remove_value_from_property(child_container_prop.name, int(
+                    row[id_column_name]), remove_if_empty_afterwards=False)
+                if old_parent.get_property(child_container_prop.name).value is None:
+                    old_parent.get_property(child_container_prop.name).value = []
 
         # Add custom label o child
-        child = child_containers.get_entity_by_id(id=int(row["BIS ID"]))
-        if _value_in_row("Custom label", row):
-            child.name = row["Custom label"]
+        child = child_containers.get_entity_by_id(id=int(row[id_column_name]))
+        if _value_in_row(get_column_header_name("custom_label_prop"), row):
+            child.name = row[get_column_header_name("custom_label_prop")]
             if child.get_property(custom_label_prop.id) is None:
                 child.add_property(id=custom_label_prop.id,
-                                   name=custom_label_prop.name, value=row["Custom label"])
+                                   name=custom_label_prop.name, value=row[get_column_header_name("custom_label_prop")])
             else:
-                child.get_property(custom_label_prop.id).value = row["Custom label"]
+                child.get_property(custom_label_prop.id).value = row[get_column_header_name("custom_label_prop")]
 
         # Treat PI
         if _value_in_row("PI", row):