lock in version 4.0.0

and don't generate python for mixs legacy or new

jsonld-context/nmdc.context.jsonld

@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from nmdc.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-05-06T11:21:32\n    Schema: NMDC\n    metamodel version: 1.7.0\n    model version: 2.1.0\n    \n    id: https://microbiomedata/schema\n    description: Schema for National Microbiome Data Collaborative (NMDC).\n  \nThis schema is organized into distinct modules:\n  \n * a set of core types for representing data values\n * the mixs schema (auto-translated from mixs excel)\n * annotation schema\n * the NMDC schema itself\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from nmdc.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-05-13T08:53:07\n    Schema: NMDC\n    metamodel version: 1.7.0\n    model version: 4.0.0\n    \n    id: https://microbiomedata/schema\n    description: Schema for National Microbiome Data Collaborative (NMDC).\nThis schema is organized into distinct modules:\n\n * a set of core types for representing data values\n * the mixs schema (auto-translated from mixs excel)\n * annotation schema\n * the NMDC schema itself\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "CAS": "http://identifiers.org/cas/",
       "CATH": "http://identifiers.org/cath/",

jsonschema/nmdc.schema.json

@@ -1230,7 +1230,7 @@
                "type": "array"
             },
             "read_based_analysis_activity_set": {
-               "description": "This property links a database object to the set of read based analysis activities.\n  ",
+               "description": "This property links a database object to the set of read based analysis activities.",
                "items": {
                   "$ref": "#/$defs/ReadBasedAnalysisActivity"
                },
@@ -3238,7 +3238,7 @@
                "type": "string"
             },
             "instrument_name": {
-               "description": "The name of the instrument that was used for processing the sample.\n   ",
+               "description": "The name of the instrument that was used for processing the sample.",
                "type": "string"
             },
             "mod_date": {
@@ -4298,6 +4298,14 @@
          "additionalProperties": false,
          "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.",
          "properties": {
+            "GOLD_sample_identifiers": {
+               "description": "identifiers for corresponding sample in GOLD",
+               "items": {
+                  "type": "string"
+               },
+               "pattern": "^GOLD:Gb[0-9]+$",
+               "type": "array"
+            },
             "GOLD_study_identifiers": {
                "description": "identifiers for corresponding project in GOLD",
                "items": {
@@ -4414,6 +4422,9 @@
                "description": "A human readable label for an entity",
                "type": "string"
             },
+            "notes": {
+               "type": "string"
+            },
             "objective": {
                "description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.",
                "type": "string"
@@ -5028,7 +5039,7 @@
          "type": "array"
       },
       "read_based_analysis_activity_set": {
-         "description": "This property links a database object to the set of read based analysis activities.\n  ",
+         "description": "This property links a database object to the set of read based analysis activities.",
          "items": {
             "$ref": "#/$defs/ReadBasedAnalysisActivity"
          },
@@ -5045,6 +5056,6 @@
    "required": [],
    "title": "NMDC",
    "type": "object",
-   "version": "2.1.0"
+   "version": "4.0.0"
 }
 

python/basic_slots.py

@@ -1,5 +1,5 @@
 # Auto generated from basic_slots.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-05-06T11:21:38
+# Generation date: 2022-05-13T08:53:13
 # Schema: NMDC-Basic-Slots
 #
 # id: https://microbiomedata/schema/basic_slots

python/core.py

@@ -1,5 +1,5 @@
 # Auto generated from core.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-05-06T11:22:17
+# Generation date: 2022-05-13T08:53:26
 # Schema: NMDC-Core
 #
 # id: https://microbiomedata/schema/core

python/nmdc.py

@@ -1,5 +1,5 @@
 # Auto generated from nmdc.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-05-06T11:22:11
+# Generation date: 2022-05-13T08:53:19
 # Schema: NMDC
 #
 # id: https://microbiomedata/schema
@@ -28,7 +28,7 @@
 from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE, XSDDateTime
 
 metamodel_version = "1.7.0"
-version = "2.1.0"
+version = "4.0.0"
 
 # Overwrite dataclasses _init_fn to add **kwargs in __init__
 dataclasses._init_fn = dataclasses_init_fn_with_kwargs
@@ -603,8 +603,10 @@ class Biosample(NamedThing):
     tot_org_carb: Optional[Union[dict, "QuantityValue"]] = None
     tot_org_c_meth: Optional[Union[dict, "TextValue"]] = None
     tot_nitro_content: Optional[Union[dict, "QuantityValue"]] = None
+    tot_nitro_cont_meth: Optional[str] = None
     tot_phosp: Optional[Union[dict, "QuantityValue"]] = None
     water_content: Optional[Union[dict, "QuantityValue"]] = None
+    water_cont_soil_meth: Optional[str] = None
     ecosystem: Optional[str] = None
     ecosystem_category: Optional[str] = None
     ecosystem_type: Optional[str] = None
@@ -628,8 +630,6 @@ class Biosample(NamedThing):
     GOLD_sample_identifiers: Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]] = empty_list()
     INSDC_biosample_identifiers: Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]] = empty_list()
     INSDC_secondary_sample_identifiers: Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]] = empty_list()
-    tot_nitro_cont_meth: Optional[str] = None
-    water_cont_soil_meth: Optional[str] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):
@@ -998,12 +998,18 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.tot_nitro_content is not None and not isinstance(self.tot_nitro_content, QuantityValue):
             self.tot_nitro_content = QuantityValue(**as_dict(self.tot_nitro_content))
 
+        if self.tot_nitro_cont_meth is not None and not isinstance(self.tot_nitro_cont_meth, str):
+            self.tot_nitro_cont_meth = str(self.tot_nitro_cont_meth)
+
         if self.tot_phosp is not None and not isinstance(self.tot_phosp, QuantityValue):
             self.tot_phosp = QuantityValue(**as_dict(self.tot_phosp))
 
         if self.water_content is not None and not isinstance(self.water_content, QuantityValue):
             self.water_content = QuantityValue(**as_dict(self.water_content))
 
+        if self.water_cont_soil_meth is not None and not isinstance(self.water_cont_soil_meth, str):
+            self.water_cont_soil_meth = str(self.water_cont_soil_meth)
+
         if self.ecosystem is not None and not isinstance(self.ecosystem, str):
             self.ecosystem = str(self.ecosystem)
 
@@ -1076,12 +1082,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
             self.INSDC_secondary_sample_identifiers = [self.INSDC_secondary_sample_identifiers] if self.INSDC_secondary_sample_identifiers is not None else []
         self.INSDC_secondary_sample_identifiers = [v if isinstance(v, ExternalIdentifier) else ExternalIdentifier(v) for v in self.INSDC_secondary_sample_identifiers]
 
-        if self.tot_nitro_cont_meth is not None and not isinstance(self.tot_nitro_cont_meth, str):
-            self.tot_nitro_cont_meth = str(self.tot_nitro_cont_meth)
-
-        if self.water_cont_soil_meth is not None and not isinstance(self.water_cont_soil_meth, str):
-            self.water_cont_soil_meth = str(self.water_cont_soil_meth)
-
         super().__post_init__(**kwargs)
 
 
@@ -1124,6 +1124,10 @@ class Study(NamedThing):
     MGnify_project_identifiers: Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]] = empty_list()
     has_credit_associations: Optional[Union[Union[dict, "CreditAssociation"], List[Union[dict, "CreditAssociation"]]]] = empty_list()
     study_image: Optional[Union[Union[dict, "ImageValue"], List[Union[dict, "ImageValue"]]]] = empty_list()
+    name: Optional[str] = None
+    description: Optional[str] = None
+    notes: Optional[str] = None
+    GOLD_sample_identifiers: Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]] = empty_list()
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):
@@ -1218,6 +1222,19 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
             self.study_image = [self.study_image] if self.study_image is not None else []
         self.study_image = [v if isinstance(v, ImageValue) else ImageValue(**as_dict(v)) for v in self.study_image]
 
+        if self.name is not None and not isinstance(self.name, str):
+            self.name = str(self.name)
+
+        if self.description is not None and not isinstance(self.description, str):
+            self.description = str(self.description)
+
+        if self.notes is not None and not isinstance(self.notes, str):
+            self.notes = str(self.notes)
+
+        if not isinstance(self.GOLD_sample_identifiers, list):
+            self.GOLD_sample_identifiers = [self.GOLD_sample_identifiers] if self.GOLD_sample_identifiers is not None else []
+        self.GOLD_sample_identifiers = [v if isinstance(v, ExternalIdentifier) else ExternalIdentifier(v) for v in self.GOLD_sample_identifiers]
+
         super().__post_init__(**kwargs)
 
 
@@ -7275,6 +7292,9 @@ class slots:
 slots.etl_software_version = Slot(uri=NMDC.etl_software_version, name="etl software version", curie=NMDC.curie('etl_software_version'),
                    model_uri=NMDC.etl_software_version, domain=None, range=Optional[str])
 
+slots.notes = Slot(uri=NMDC.notes, name="notes", curie=NMDC.curie('notes'),
+                   model_uri=NMDC.notes, domain=None, range=Optional[str])
+
 slots.metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="metabolite quantified", curie=NMDC.curie('metabolite_quantified'),
                    model_uri=NMDC.metabolite_quantified, domain=None, range=Optional[Union[str, ChemicalEntityId]])
 
@@ -7425,6 +7445,29 @@ class slots:
 slots.study_doi = Slot(uri=NMDC.doi, name="study_doi", curie=NMDC.curie('doi'),
                    model_uri=NMDC.study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]])
 
+slots.study_name = Slot(uri=NMDC.name, name="study_name", curie=NMDC.curie('name'),
+                   model_uri=NMDC.study_name, domain=Study, range=Optional[str])
+
+slots.study_websites = Slot(uri=NMDC.websites, name="study_websites", curie=NMDC.curie('websites'),
+                   model_uri=NMDC.study_websites, domain=Study, range=Optional[Union[str, List[str]]])
+
+slots.study_description = Slot(uri=DCTERMS.description, name="study_description", curie=DCTERMS.curie('description'),
+                   model_uri=NMDC.study_description, domain=Study, range=Optional[str])
+
+slots.study_notes = Slot(uri=NMDC.notes, name="study_notes", curie=NMDC.curie('notes'),
+                   model_uri=NMDC.study_notes, domain=Study, range=Optional[str])
+
+slots.study_alternative_names = Slot(uri=NMDC.alternative_names, name="study_alternative names", curie=NMDC.curie('alternative_names'),
+                   model_uri=NMDC.study_alternative_names, domain=Study, range=Optional[Union[str, List[str]]])
+
+slots.study_GOLD_sample_identifiers = Slot(uri=NMDC.GOLD_sample_identifiers, name="study_GOLD sample identifiers", curie=NMDC.curie('GOLD_sample_identifiers'),
+                   model_uri=NMDC.study_GOLD_sample_identifiers, domain=Study, range=Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^GOLD:Gb[0-9]+$'))
+
+slots.study_INSDC_bioproject_identifiers = Slot(uri=NMDC.INSDC_bioproject_identifiers, name="study_INSDC bioproject identifiers", curie=NMDC.curie('INSDC_bioproject_identifiers'),
+                   model_uri=NMDC.study_INSDC_bioproject_identifiers, domain=Study, range=Optional[Union[Union[str, ExternalIdentifier], List[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^bioproject:PRJ[DEN][A-Z][0-9]+$'))
+
 slots.biosample_processing_has_input = Slot(uri=NMDC.has_input, name="biosample processing_has input", curie=NMDC.curie('has_input'),
                    model_uri=NMDC.biosample_processing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]])
 

python/workflow_execution_activity.py

@@ -1,5 +1,5 @@
 # Auto generated from workflow_execution_activity.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-05-06T11:22:05
+# Generation date: 2022-05-13T08:53:16
 # Schema: NMDC-Workflow-Exectution
 #
 # id: https://microbiomedata/schema/workflow_execution_activity