Merge pull request #2338 from microbiomedata/2336-deprecate-protocolexecution

Deprecate `ProtocolExecution` class and related slots

Author: bmeluch

project.Makefile

@@ -159,7 +159,6 @@ local/mongo_as_unvalidated_nmdc_database.yaml:
 		--selected-collections instrument_set \
 		--selected-collections material_processing_set \
 		--selected-collections processed_sample_set \
-		--selected-collections protocol_execution_set \
 		--selected-collections storage_process_set \
 		--selected-collections study_set \
 		--selected-collections workflow_execution_set \

src/data/invalid/ProtocolExecution-inlined_not_valid.yaml

@@ -116,30 +116,3 @@ material_processing_set:
       type: nmdc:QuantityValue
       has_unit: 'uL'
       has_numeric_value: 5
-protocol_execution_set:
-  - id: nmdc:pex-12-123
-    type: nmdc:ProtocolExecution
-    has_input:
-      - nmdc:bsm-00-435737
-    has_process_parts:
-      - nmdc:dispro-99-123
-      - nmdc:chcpr-99-123
-      - nmdc:filtpr-00-123
-    protocol_execution_category: organic_matter_extraction
-    protocol_link:
-      type: nmdc:Protocol
-      name: Organic Matter Extraction Analytical Processes
-      url: https://pnnl.sharepoint.com/:w:/r/sites/EMSL/_layouts/15/Doc.aspx?sourcedoc=%7B06286DC5-9E52-4CF9-B583-F8BE695F60D9%7D&file=Protocol_WEOM.docx&action=default&mobileredirect=true
-  - id: nmdc:pex-12-3456
-    type: nmdc:ProtocolExecution
-    has_input:
-      - nmdc:procsm-00-3
-    has_process_parts:
-      - nmdc:cspro-99-456
-      - nmdc:dispro-99-456
-      - nmdc:chcpr-99-456
-    protocol_execution_category: solid_phase_extraction
-    protocol_link:
-      type: nmdc:Protocol
-      name: Organic Matter Solid Phase Extraction Analytical Processes
-      url: https://pnnl.sharepoint.com/sites/EMSL/Shared%20Documents/Forms/AllItems.aspx?id=%2Fsites%2FEMSL%2FShared%20Documents%2FScience%20and%20Technology%2FScience%20Areas%2FEnvironmental%20Transformations%20%26%20Interactions%20Group%2FResearch%20Campaigns%2FFY21%2F1000%20Soil%20Pilot%2Fprotocols%2FFTICR%2DMS%2FFTICRMS%2DGilsonAutomatedSPESOP%2D130521%2D1547%2D150%2Epdf&parent=%2Fsites%2FEMSL%2FShared%20Documents%2FScience%20and%20Technology%2FScience%20Areas%2FEnvironmental%20Transformations%20%26%20Interactions%20Group%2FResearch%20Campaigns%2FFY21%2F1000%20Soil%20Pilot%2Fprotocols%2FFTICR%2DMS

src/data/valid/Database-NOM-material-processing.yaml

@@ -109,19 +109,6 @@ storage_process_set:
       - nmdc:procsm-78-BZAPKH
     type: nmdc:StorageProcess
 
-protocol_execution_set:
-  - id: nmdc:pex-99-18sD2
-    type: nmdc:ProtocolExecution
-    has_input:
-      - nmdc:bsm-65-0002
-    has_process_parts:
-      - nmdc:extrp-71-r2pk
-      - nmdc:filtpr-22-32G2BS
-    protocol_execution_category: organic_matter_extraction
-    protocol_link:
-      type: nmdc:Protocol
-      url: https://www.protocols.io/view/water-extractable-organic-matter-weom-ewov1o4oylr2/v1
-      name: Water Extractable Organic Matter (WEOM)
 material_processing_set:
   - id: nmdc:cspro-99-xyzxyz
     type: nmdc:ChromatographicSeparationProcess

src/data/valid/Database-interleaved.yaml

@@ -349,7 +349,6 @@ classes:
       - manifest_set
       - material_processing_set
       - processed_sample_set
-      - protocol_execution_set
       - storage_process_set
       - study_set
       - workflow_execution_set
@@ -503,6 +502,7 @@ classes:
           syntax: "{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$"
           interpolated: true
         description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.
+    deprecated: "not used, not fulfilling intended purpose https://github.com/microbiomedata/nmdc-schema/issues/2336"
 
   SubSamplingProcess:
     class_uri: 'nmdc:SubSamplingProcess'
@@ -1239,6 +1239,7 @@ slots:
     mixins: object_set
     range: ProtocolExecution
     description: This property links a database object to the set of protocol executions within it.
+    deprecated: "not used https://github.com/microbiomedata/nmdc-schema/issues/2336"
 
   storage_process_set:
     mixins: object_set
@@ -1280,13 +1281,15 @@ slots:
   protocol_execution_category:
     range: ProtocolCategoryEnum
     required: true
+    deprecated: "not used https://github.com/microbiomedata/nmdc-schema/issues/2336"
 
   has_process_parts:
     range: PlannedProcess
     description: A list of process parts that make up a protocol.
     required: true
     multivalued: true
     list_elements_ordered: true
+    deprecated: "not used https://github.com/microbiomedata/nmdc-schema/issues/2336"
 
   filter_material:
     description: "A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained."