From 001cbad3224d90aa9eda2a49d10c68ae1d7c83ed Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 11:05:26 -0800 Subject: [PATCH 01/12] remove Activity from prov.yaml --- src/schema/prov.yaml | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/src/schema/prov.yaml b/src/schema/prov.yaml index d2554fc6e1..64b372a83e 100644 --- a/src/schema/prov.yaml +++ b/src/schema/prov.yaml @@ -18,29 +18,6 @@ default_range: string classes: - Activity: - description: Something that occurs over a period of time and acts upon or with entities; - it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. - slots: - - id - - name - - started_at_time - - ended_at_time - - was_informed_by - - used - comments: - - to be replaced with PlannedProcess in the monterey-schema - notes: - - removed was_associated_with because we are trying to avoid instantiating id-less Agents - mappings: - - prov:Activity - slot_usage: - id: - required: true - structured_pattern: - syntax: "{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}" - interpolated: true - slots: started_at_time: From 484698935ef385add992c63abcfa3b2589a06444 Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 11:05:51 -0800 Subject: [PATCH 02/12] move Activity slots over WorkflowExecutionActivity --- src/schema/workflow_execution_activity.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 024b63563f..1e3b02fff9 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -37,6 +37,12 @@ classes: embl.ena: >- An analysis contains secondary analysis results derived from sequence reads (e.g. a genome assembly) slots: + - id + - name + - started_at_time + - ended_at_time + - was_informed_by + - used - execution_resource - git_url - has_input From b4bfe852a6ab933f93f5d9d8cb460b581c9e014d Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 11:06:41 -0800 Subject: [PATCH 03/12] remove is_a:Activity from WorkflowExecutionActivity --- src/schema/workflow_execution_activity.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 1e3b02fff9..e34233f616 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -28,7 +28,6 @@ classes: - analysis comments: - Each instance of this (and all other) activities is a distinct run with start and stop times, potentially with different inputs and outputs - is_a: Activity in_subset: - workflow subset description: >- From e858e1bc1fb87365b4a00d8437b86ea9c62e1bc8 Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 11:07:59 -0800 Subject: [PATCH 04/12] update comments for WorkflowExecutionActivity --- src/schema/workflow_execution_activity.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index e34233f616..77d408ebf8 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -27,7 +27,7 @@ classes: aliases: - analysis comments: - - Each instance of this (and all other) activities is a distinct run with start and stop times, potentially with different inputs and outputs + - Each instance of this (and all other) subclasses of WorkflowExecution is a distinct run with start and stop times, potentially with different inputs and outputs in_subset: - workflow subset description: >- From 75878649733029a5ef158a775bfbc41ad2447005 Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 11:34:34 -0800 Subject: [PATCH 05/12] change domain of execution_resource to WorkflowExecutionActivity --- src/schema/core.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index d12a510299..e580478217 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -592,7 +592,7 @@ slots: description: Links a resource to another resource that either logically or physically includes it. execution_resource: - domain: Activity + domain: WorkflowExecutionActivity range: string # is_a: attribute examples: From 3a5b2af076c7829e97697ae52c58ff198f1c544b Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 11:39:59 -0800 Subject: [PATCH 06/12] remove activity_set --- src/schema/nmdc.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 5d3bc835b7..8f6bd714a3 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -2767,11 +2767,6 @@ slots: description: This property links a database object to the set of all functional annotations - activity_set: - domain: Database # not inherited byt mixin users - mixins: object_set - range: WorkflowExecutionActivity - description: This property links a database object to the set of workflow activities. mags_activity_set: domain: Database # not inherited byt mixin users mixins: object_set From 2e6aa365f226629b9506e6baf2363b057ab122cc Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 12:09:14 -0800 Subject: [PATCH 07/12] change activity_set to workflow_execution_activity_set --- src/schema/nmdc.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 8f6bd714a3..750a054aca 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -2767,6 +2767,11 @@ slots: description: This property links a database object to the set of all functional annotations + workflow_execution_activity_set: + domain: Database # not inherited byt mixin users + mixins: object_set + range: WorkflowExecutionActivity + description: This property links a database object to the set of workflow activities. mags_activity_set: domain: Database # not inherited byt mixin users mixins: object_set From c714b680deb20de45f75d405fb28b3e0461bd02d Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 12:13:15 -0800 Subject: [PATCH 08/12] remove activity_set from Database slots in nmdc.yaml --- src/schema/nmdc.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 750a054aca..32970623d3 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -192,7 +192,6 @@ classes: # - material_sample_set # - material_sampling_activity_set # - reaction_activity_set - - activity_set - biosample_set - collecting_biosamples_from_site_set - data_object_set From f86a1b33a9256490992f42b0dc0a57974b16bcf7 Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 12:14:18 -0800 Subject: [PATCH 09/12] change domain of Activity to WorkflowExecutionActivity --- src/schema/workflow_execution_activity.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 77d408ebf8..bbebb50161 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -560,5 +560,5 @@ slots: multivalued: true version: - domain: Activity + domain: WorkflowExecutionActivity range: string From 481e038b0cd6241c29029e325877ee42f9d15baf Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 13:03:46 -0800 Subject: [PATCH 10/12] change domain of started_at_time --- src/schema/prov.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/schema/prov.yaml b/src/schema/prov.yaml index 64b372a83e..fbfe84d0e8 100644 --- a/src/schema/prov.yaml +++ b/src/schema/prov.yaml @@ -21,7 +21,7 @@ classes: slots: started_at_time: - domain: Activity + domain: WorkflowExecutionActivity range: string # range: datetime pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$ @@ -32,7 +32,7 @@ slots: - prov:startedAtTime ended_at_time: - domain: Activity + domain: WorkflowExecutionActivity # range: datetime pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$ notes: >- @@ -42,17 +42,17 @@ slots: - prov:endedAtTime was_informed_by: - domain: Activity - range: Activity + domain: WorkflowExecutionActivity + range: WorkflowExecutionActivity mappings: - prov:wasInformedBy was_generated_by: - range: Activity + range: WorkflowExecutionActivity mappings: - prov:wasGeneratedBy used: - domain: Activity + domain: WorkflowExecutionActivity mappings: - prov:used From 25db7614ea2b326865fc7d0c6a6fea5ae833b4ce Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 13:08:28 -0800 Subject: [PATCH 11/12] change to worklow_execution_set --- src/data/valid/Database-img_mg_annotation_objects.yaml | 2 +- src/schema/nmdc.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/data/valid/Database-img_mg_annotation_objects.yaml b/src/data/valid/Database-img_mg_annotation_objects.yaml index 692d04b7df..38e69f71d7 100644 --- a/src/data/valid/Database-img_mg_annotation_objects.yaml +++ b/src/data/valid/Database-img_mg_annotation_objects.yaml @@ -1,4 +1,4 @@ -activity_set: +workflow_execution_set: - has_input: - nmdc:b4b798cc9e7e9253ae8256a8237fd371 git_url: https://img.jgi.doe.gov diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 32970623d3..7c890214a5 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -2766,7 +2766,7 @@ slots: description: This property links a database object to the set of all functional annotations - workflow_execution_activity_set: + workflow_execution_set: domain: Database # not inherited byt mixin users mixins: object_set range: WorkflowExecutionActivity From 8675ae3737acf258d75424b76f2fecdfa2734044 Mon Sep 17 00:00:00 2001 From: "brynn.zalmanek@pnnl.gov" Date: Wed, 13 Dec 2023 13:26:34 -0800 Subject: [PATCH 12/12] add workflow_execution_set slot to Database class --- src/schema/nmdc.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 7c890214a5..aa5ed918c3 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -216,8 +216,7 @@ classes: - read_based_taxonomy_analysis_activity_set - read_qc_analysis_activity_set - study_set - - + - workflow_execution_set Pooling: class_uri: nmdc:Pooling