commiting v9.0.4 generated artifacts to main

microbiomedata · Nov 3, 2023 · b3a6a46 · b3a6a46
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diff --git a/assets/filtered-api-requests/filtered-request-validation-log.txt b/assets/filtered-api-requests/filtered-request-validation-log.txt
@@ -477,4 +477,5 @@
 ✗ 'emsl:output_512117' does not match '^nmdc:dobj-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$' in $.omics_processing_set[476].has_output[0]
 ✗ 'emsl:output_512118' does not match '^nmdc:dobj-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$' in $.omics_processing_set[477].has_output[0]
 ✗ 'emsl:output_512114' does not match '^nmdc:dobj-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$' in $.omics_processing_set[478].has_output[0]
+✗ Additional properties are not allowed ('award_dois', 'publication_dois' were unexpected) in $.study_set[0]
 ✗ 'study_category' is a required property in $.study_set[0]
diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py
@@ -1,5 +1,5 @@
 # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1
-# Generation date: 2023-11-01T18:11:24
+# Generation date: 2023-11-03T15:42:11
 # Schema: NMDC
 #
 # id: https://w3id.org/nmdc/nmdc
@@ -31,7 +31,7 @@
 from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE
 
 metamodel_version = "1.7.0"
-version = "v9.0.2"
+version = "v9.0.4"
 
 # Overwrite dataclasses _init_fn to add **kwargs in __init__
 dataclasses._init_fn = dataclasses_init_fn_with_kwargs
@@ -888,7 +888,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.description is not None and not isinstance(self.description, str):
             self.description = str(self.description)
 
-        self._normalize_inlined_as_dict(slot_name="associated_dois", slot_type=Doi, key_name="doi_value", keyed=False)
+        if not isinstance(self.associated_dois, list):
+            self.associated_dois = [self.associated_dois] if self.associated_dois is not None else []
+        self.associated_dois = [v if isinstance(v, Doi) else Doi(**as_dict(v)) for v in self.associated_dois]
 
         if self.ecosystem is not None and not isinstance(self.ecosystem, str):
             self.ecosystem = str(self.ecosystem)
@@ -8566,9 +8568,6 @@ class slots:
 slots.notes = Slot(uri=NMDC.notes, name="notes", curie=NMDC.curie('notes'),
                    model_uri=NMDC.notes, domain=None, range=Optional[str])
 
-slots.canary = Slot(uri=NMDC.canary, name="canary", curie=NMDC.curie('canary'),
-                   model_uri=NMDC.canary, domain=None, range=Optional[str])
-
 slots.ess_dive_datasets = Slot(uri=NMDC.ess_dive_datasets, name="ess_dive_datasets", curie=NMDC.curie('ess_dive_datasets'),
                    model_uri=NMDC.ess_dive_datasets, domain=None, range=Optional[Union[str, List[str]]])
 
@@ -8702,17 +8701,17 @@ class slots:
                    model_uri=NMDC.principal_investigator, domain=None, range=Optional[Union[dict, PersonValue]])
 
 slots.associated_dois = Slot(uri=NMDC.associated_dois, name="associated_dois", curie=NMDC.curie('associated_dois'),
-                   model_uri=NMDC.associated_dois, domain=None, range=Optional[Union[Union[dict, Doi], List[Union[dict, Doi]]]])
+                   model_uri=NMDC.associated_dois, domain=Study, range=Optional[Union[Union[dict, Doi], List[Union[dict, Doi]]]])
 
 slots.doi_value = Slot(uri=NMDC.doi_value, name="doi_value", curie=NMDC.curie('doi_value'),
-                   model_uri=NMDC.doi_value, domain=None, range=Union[str, URIorCURIE],
+                   model_uri=NMDC.doi_value, domain=Doi, range=Union[str, URIorCURIE],
                    pattern=re.compile(r'^doi:10.\d{2,9}/.*$'))
 
 slots.doi_provider = Slot(uri=NMDC.doi_provider, name="doi_provider", curie=NMDC.curie('doi_provider'),
-                   model_uri=NMDC.doi_provider, domain=None, range=Optional[Union[str, "DoiProviderEnum"]])
+                   model_uri=NMDC.doi_provider, domain=Doi, range=Optional[Union[str, "DoiProviderEnum"]])
 
 slots.doi_category = Slot(uri=NMDC.doi_category, name="doi_category", curie=NMDC.curie('doi_category'),
-                   model_uri=NMDC.doi_category, domain=None, range=Union[str, "DoiCategoryEnum"])
+                   model_uri=NMDC.doi_category, domain=Doi, range=Union[str, "DoiCategoryEnum"])
 
 slots.dois = Slot(uri=NMDC.dois, name="dois", curie=NMDC.curie('dois'),
                    model_uri=NMDC.dois, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]],

diff --git a/nmdc_schema/nmdc.schema.json b/nmdc_schema/nmdc.schema.json
@@ -3672,7 +3672,7 @@
         },
         "Doi": {
             "additionalProperties": false,
-            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation.  The DOI system is particularly used for electronic documents.",
+            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.",
             "if": {
                 "properties": {
                     "doi_category": {
@@ -8382,5 +8382,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "v9.0.2"
+    "version": "v9.0.4"
 }
diff --git a/nmdc_schema/nmdc_materialized_patterns.schema.json b/nmdc_schema/nmdc_materialized_patterns.schema.json
@@ -3672,7 +3672,7 @@
         },
         "Doi": {
             "additionalProperties": false,
-            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation.  The DOI system is particularly used for electronic documents.",
+            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.",
             "if": {
                 "properties": {
                     "doi_category": {
@@ -8382,5 +8382,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "v9.0.2"
+    "version": "v9.0.4"
 }
diff --git a/nmdc_schema/nmdc_materialized_patterns.yaml b/nmdc_schema/nmdc_materialized_patterns.yaml
@@ -11,7 +11,7 @@ notes:
 - not importing any MIxS terms where the relationship between the name (SCN) and the
   id isn't 1:1
 id: https://w3id.org/nmdc/nmdc
-version: v9.0.2
+version: v9.0.4
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
   FMA:
@@ -3757,11 +3757,6 @@ slots:
     name: notes
     description: from study class
     from_schema: https://w3id.org/nmdc/nmdc
-  canary:
-    name: canary
-    description: a slot that can be added and removed as evidence that schema changes
-      have propagated to other systems
-    from_schema: https://w3id.org/nmdc/nmdc
   ess_dive_datasets:
     name: ess_dive_datasets
     description: List of ESS-DIVE dataset DOIs
@@ -4181,8 +4176,10 @@ slots:
     aliases:
     - Associated DOIs
     - Associated digital object identifiers
+    domain: Study
     multivalued: true
     range: Doi
+    inlined_as_list: true
   doi_value:
     name: doi_value
     description: A digital object identifier, which is intended to persistantly identify
@@ -4200,6 +4197,7 @@ slots:
     - OBI:0002110
     narrow_mappings:
     - edam.data:1188
+    domain: Doi
     range: uriorcurie
     required: true
     pattern: ^doi:10.\d{2,9}/.*$
@@ -4214,6 +4212,7 @@ slots:
     from_schema: https://w3id.org/nmdc/nmdc
     close_mappings:
     - NCIT:C74932
+    domain: Doi
     range: DoiProviderEnum
   doi_category:
     name: doi_category
@@ -4224,6 +4223,7 @@ slots:
     in_subset:
     - data_portal_subset
     from_schema: https://w3id.org/nmdc/nmdc
+    domain: Doi
     range: DoiCategoryEnum
     required: true
   dois:
@@ -18693,8 +18693,6 @@ classes:
         name: part_of
         range: Study
         required: true
-        inlined: false
-        inlined_as_list: false
         pattern: ^nmdc:sty-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$
       fire:
         name: fire
@@ -19071,7 +19069,7 @@ classes:
   Doi:
     name: Doi
     description: A centrally registered identifier symbol used to uniquely identify
-      objects given by the International DOI Foundation.  The DOI system is particularly
+      objects given by the International DOI Foundation. The DOI system is particularly
       used for electronic documents.
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:

diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.py b/nmdc_schema/nmdc_schema_accepting_legacy_ids.py
@@ -1,5 +1,5 @@
 # Auto generated from nmdc_schema_accepting_legacy_ids.yaml by pythongen.py version: 0.0.1
-# Generation date: 2023-11-03T14:14:18
+# Generation date: 2023-11-03T15:43:37
 # Schema: NMDC
 #
 # id: https://w3id.org/nmdc/nmdc

diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json b/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json
@@ -3672,7 +3672,7 @@
         },
         "Doi": {
             "additionalProperties": false,
-            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation.  The DOI system is particularly used for electronic documents.",
+            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.",
             "if": {
                 "properties": {
                     "doi_category": {
@@ -8382,5 +8382,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "v9.0.2"
+    "version": "v9.0.4"
 }
diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml b/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml
@@ -11,7 +11,7 @@ notes:
 - not importing any MIxS terms where the relationship between the name (SCN) and the
   id isn't 1:1
 id: https://w3id.org/nmdc/nmdc
-version: v9.0.2
+version: v9.0.4
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
   FMA:
@@ -3757,11 +3757,6 @@ slots:
     name: notes
     description: from study class
     from_schema: https://w3id.org/nmdc/nmdc
-  canary:
-    name: canary
-    description: a slot that can be added and removed as evidence that schema changes
-      have propagated to other systems
-    from_schema: https://w3id.org/nmdc/nmdc
   ess_dive_datasets:
     name: ess_dive_datasets
     description: List of ESS-DIVE dataset DOIs
@@ -4181,8 +4176,10 @@ slots:
     aliases:
     - Associated DOIs
     - Associated digital object identifiers
+    domain: Study
     multivalued: true
     range: Doi
+    inlined_as_list: true
   doi_value:
     name: doi_value
     description: A digital object identifier, which is intended to persistantly identify
@@ -4200,6 +4197,7 @@ slots:
     - OBI:0002110
     narrow_mappings:
     - edam.data:1188
+    domain: Doi
     range: uriorcurie
     required: true
     pattern: ^doi:10.\d{2,9}/.*$
@@ -4214,6 +4212,7 @@ slots:
     from_schema: https://w3id.org/nmdc/nmdc
     close_mappings:
     - NCIT:C74932
+    domain: Doi
     range: DoiProviderEnum
   doi_category:
     name: doi_category
@@ -4224,6 +4223,7 @@ slots:
     in_subset:
     - data_portal_subset
     from_schema: https://w3id.org/nmdc/nmdc
+    domain: Doi
     range: DoiCategoryEnum
     required: true
   dois:
@@ -18693,8 +18693,6 @@ classes:
         name: part_of
         range: Study
         required: true
-        inlined: false
-        inlined_as_list: false
         pattern: .*
       fire:
         name: fire
@@ -19071,7 +19069,7 @@ classes:
   Doi:
     name: Doi
     description: A centrally registered identifier symbol used to uniquely identify
-      objects given by the International DOI Foundation.  The DOI system is particularly
+      objects given by the International DOI Foundation. The DOI system is particularly
       used for electronic documents.
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:

diff --git a/nmdc_schema/nmdc_schema_merged.yaml b/nmdc_schema/nmdc_schema_merged.yaml
@@ -11,7 +11,7 @@ notes:
 - not importing any MIxS terms where the relationship between the name (SCN) and the
   id isn't 1:1
 id: https://w3id.org/nmdc/nmdc
-version: v9.0.2
+version: v9.0.4
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
   FMA:
@@ -3757,11 +3757,6 @@ slots:
     name: notes
     description: from study class
     from_schema: https://w3id.org/nmdc/nmdc
-  canary:
-    name: canary
-    description: a slot that can be added and removed as evidence that schema changes
-      have propagated to other systems
-    from_schema: https://w3id.org/nmdc/nmdc
   ess_dive_datasets:
     name: ess_dive_datasets
     description: List of ESS-DIVE dataset DOIs
@@ -4181,8 +4176,10 @@ slots:
     aliases:
     - Associated DOIs
     - Associated digital object identifiers
+    domain: Study
     multivalued: true
     range: Doi
+    inlined_as_list: true
   doi_value:
     name: doi_value
     description: A digital object identifier, which is intended to persistantly identify
@@ -4200,6 +4197,7 @@ slots:
     - OBI:0002110
     narrow_mappings:
     - edam.data:1188
+    domain: Doi
     range: uriorcurie
     required: true
     pattern: ^doi:10.\d{2,9}/.*$
@@ -4214,6 +4212,7 @@ slots:
     from_schema: https://w3id.org/nmdc/nmdc
     close_mappings:
     - NCIT:C74932
+    domain: Doi
     range: DoiProviderEnum
   doi_category:
     name: doi_category
@@ -4224,6 +4223,7 @@ slots:
     in_subset:
     - data_portal_subset
     from_schema: https://w3id.org/nmdc/nmdc
+    domain: Doi
     range: DoiCategoryEnum
     required: true
   dois:
@@ -18686,8 +18686,6 @@ classes:
         name: part_of
         range: Study
         required: true
-        inlined: false
-        inlined_as_list: false
         pattern: ^nmdc:sty-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$
       fire:
         name: fire
@@ -19064,7 +19062,7 @@ classes:
   Doi:
     name: Doi
     description: A centrally registered identifier symbol used to uniquely identify
-      objects given by the International DOI Foundation.  The DOI system is particularly
+      objects given by the International DOI Foundation. The DOI system is particularly
       used for electronic documents.
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:

diff --git a/project/jsonld/nmdc.context.jsonld b/project/jsonld/nmdc.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-11-01T18:11:07",
+      "generation_date": "2023-11-03T15:41:53",
       "source": "nmdc.yaml"
    },
    "@context": {

diff --git a/project/jsonschema/nmdc.schema.json b/project/jsonschema/nmdc.schema.json
@@ -3672,7 +3672,7 @@
         },
         "Doi": {
             "additionalProperties": false,
-            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation.  The DOI system is particularly used for electronic documents.",
+            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.",
             "if": {
                 "properties": {
                     "doi_category": {
@@ -8382,5 +8382,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "v9.0.2"
+    "version": "v9.0.4"
 }
diff --git a/project/nmdc_materialized_patterns.schema.json b/project/nmdc_materialized_patterns.schema.json
@@ -3672,7 +3672,7 @@
         },
         "Doi": {
             "additionalProperties": false,
-            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation.  The DOI system is particularly used for electronic documents.",
+            "description": "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.",
             "if": {
                 "properties": {
                     "doi_category": {
@@ -8382,5 +8382,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "v9.0.2"
+    "version": "v9.0.4"
 }