diff --git a/project.Makefile b/project.Makefile index d657903cc5..a8e9497b93 100644 --- a/project.Makefile +++ b/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 \ diff --git a/src/data/invalid/ProtocolExecution-inlined_not_valid.yaml b/src/data/invalid/ProtocolExecution-inlined_not_valid.yaml deleted file mode 100644 index 0012f2405e..0000000000 --- a/src/data/invalid/ProtocolExecution-inlined_not_valid.yaml +++ /dev/null @@ -1,22 +0,0 @@ -id: nmdc:pex-99-18sD2 -type: nmdc:ProtocolExecution -has_input: - - nmdc:bsm-11-34db -has_process_parts: - - id: "nmdc:extrp-71-r2pk" - has_input: - - "nmdc:ome-6" - has_output: - - "nmdc:ome-8" - extractant: - has_solution_components: - - compound: deionized_water - - compound: methanol - concentration: - has_numeric_value: 5 - has_unit: "%" -protocol_execution_category: organic_matter_extraction -protocol_link: - url: https://www.protocols.io/view/water-extractable-organic-matter-weom-ewov1o4oylr2/v1 - name: Water Extractable Organic Matter (WEOM) - type: nmdc:Protocol diff --git a/src/data/valid/Database-NOM-material-processing.yaml b/src/data/valid/Database-NOM-material-processing.yaml index c04f961142..3e6e0a1e56 100644 --- a/src/data/valid/Database-NOM-material-processing.yaml +++ b/src/data/valid/Database-NOM-material-processing.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 diff --git a/src/data/valid/Database-interleaved.yaml b/src/data/valid/Database-interleaved.yaml index 83ed635885..be0d7e2221 100644 --- a/src/data/valid/Database-interleaved.yaml +++ b/src/data/valid/Database-interleaved.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 diff --git a/src/data/valid/ProtocolExecution-minimal.yaml b/src/data/valid/ProtocolExecution-minimal.yaml deleted file mode 100644 index 3645f0ac27..0000000000 --- a/src/data/valid/ProtocolExecution-minimal.yaml +++ /dev/null @@ -1,12 +0,0 @@ -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) \ No newline at end of file diff --git a/src/data/valid/ProtocolExecution-single_step.yaml b/src/data/valid/ProtocolExecution-single_step.yaml deleted file mode 100644 index 5d6f9a188a..0000000000 --- a/src/data/valid/ProtocolExecution-single_step.yaml +++ /dev/null @@ -1,11 +0,0 @@ -id: nmdc:pex-99-18sD2 -type: nmdc:ProtocolExecution -has_input: - - nmdc:bsm-65-0002 -has_process_parts: - - nmdc:extrp-71-r2pk -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) \ No newline at end of file diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 160d58f329..fd0bb1871f 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.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 @@ -1280,6 +1281,7 @@ slots: protocol_execution_category: range: ProtocolCategoryEnum required: true + deprecated: "not used https://github.com/microbiomedata/nmdc-schema/issues/2336" has_process_parts: range: PlannedProcess @@ -1287,6 +1289,7 @@ slots: 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."