FIX: in consistencies in csv treatment

README.md

@@ -66,6 +66,19 @@ stored in LinkAhead
 You can create a filled CSV template with the information about Containers as
 it is currently stored in LinkAhead.
 
+### Extensibility
+The registration, update and export does not only work with RecordTypes and
+Properties that are defined within this module, but the data model can be
+extended by users of the system: Any Property that is added to the Sample
+RecordType can also be used within the workflow. Once an additional Property
+was added to the RecordType (say "width"), you can select a corresponding
+column during registration with the same name and also upload CSV templates
+that have this column. The Sample records will be created or updated to also
+have this ("width") column.
+
+If the Property that is added is a RecordType, it must be kind of an enum, i.e.
+it should be uniquely identified either by its name or by a sole property.
+
 ## Usage
 
 **TODO**: Add explanations, screenshots, ec. to explain the sample
@@ -132,7 +145,7 @@ allow to change those.
 This is the central RecordType for the sample management and used to represent
 samples of various types
 
-#### `Parent_Sample` (`$parent_sample_prop`)
+#### `Parent_sample` (`$parent_sample_prop`)
 references the sample from which the sample at hand originated (for example by
 cutting the parent sample into multiple pieces0
 

models_and_helper_scripts/sample-management-datamodel.yml

@@ -83,7 +83,7 @@ Sample:
   recommended_properties:
     Container:
     SampleType:
-    Parent_Sample:
+    Parent_sample:
       datatype: Sample
     Main User:
       datatype: Person

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

@@ -42,6 +42,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
         "Latitude start",
         "Longitude start",
         "Elevation start",
+        "Start date",
         "Storage ID",
         "Device"
     ];
@@ -73,8 +74,10 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
 
     const unused_property_names = [
         "Main User",
+        "Event",
+        "Container",
         'NagoyaCase',
-        "Parent_Sample",
+        "Parent_sample",
     ]
 
     const upload_sample_template_form_config = {

sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml

@@ -68,7 +68,7 @@ entity_names:
   labelcounter_prop: counter
   labelcounter_rt: LabelCounter
   last_name_prop: last_name
-  parent_sample_prop: Parent_Sample
+  parent_sample_prop: Parent_sample
   responsible_rt: Responsible
   start_date_prop: start_date
   locality_description_prop: locality_description

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

@@ -33,10 +33,16 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
     """
 
     main_user_prop = db.get_entity_by_name(get_entity_name("Main User"))
+    pi_prop = db.get_entity_by_name(get_entity_name("PI"))
     container_rt = db.get_entity_by_name(get_entity_name("container_rt"))
     device_rt = db.get_entity_by_name(get_entity_name("Device"))
     parent_sample_prop = db.get_entity_by_name(get_entity_name("parent_sample_prop"))
 
+    if (get_column_header_name("PI") in data and
+            return_value_if_not_none(data[get_column_header_name("PI")]) is not None):
+        pi_user = get_person(return_value_if_not_none(data[get_column_header_name("PI")]))
+        sample = update_property(sample, pi_prop.id, pi_user, property_name=pi_prop.name)
+
     if (get_column_header_name("Main User") in data and
             return_value_if_not_none(data[get_column_header_name("Main User")]) is not None):
         main_user = get_person(return_value_if_not_none(data[get_column_header_name("Main User")]))

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

@@ -79,6 +79,7 @@ DATATYPE_DEFINITIONS = use_custom_names({
 # Must exist
 OBLIGATORY_COLUMNS = use_custom_names([
     "entity_id",
+    "Start date",
 ])
 
 OBLIGATORY_COLUMNS_CHILD = use_custom_names([
@@ -114,6 +115,7 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
     "Longitude start",
     "Longitude stop",
     "Main User",
+    "PI",
     "PDFReport",
     "parent_sample_prop",
     "Sphere",
@@ -124,6 +126,6 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
 
 IGNORED_COLUMN_NAMES_SAMPLE = use_custom_names([
     "LinkAhead URL",
-    "Parent Sample",
+    "Parent_sample",
     "Storage chain",
 ])

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

@@ -21,6 +21,7 @@ from caosadvancedtools.datainconsistency import DataInconsistencyError
 
 from .utils import get_entity_name
 
+from linkahead.cached import cached_get_entity_by, cached_query as cquery
 
 def get_person(text: str) -> db.Record:
     """Return the Person Record that is specifed as 'Main User' or
@@ -60,11 +61,19 @@ def _get_person_by_fullname(first_name: str, last_name: str) -> db.Record:
         return res[0]
 
 
-def _get_person_by_id(eid: str) -> db.Record:
-
-    try:
-        return db.get_entity_by_id(eid, role=get_entity_name("Person"))
-    except db.EmptyUniqueQueryError:
+def _get_person_by_id(ident: str) -> db.Record:
+    options = cquery(f"FIND '{get_entity_name('Person')}' WITH ID='{ident}' ")
+    if len(options)==1:
+        return options[0]
+    options = cquery(f"FIND '{get_entity_name('Person')}' WITH "
+        f"'{get_entity_name('abbreviation_prop')}'='{ident}' ")
+    if len(options) == 1:
+        return options[0]
+    elif len(options) == 0:
+        raise DataInconsistencyError(
+            f"Could not find a {get_entity_name('Person')} with ID {ident}."
+        )
+    else:
         raise DataInconsistencyError(
-            f"Could not find a {get_entity_name('Person')} with ID {eid}."
+            f"Found multiple {get_entity_name('Person')} with {get_entity_name('abbreviation_prop')}={ident}."
         )