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Merge pull request #2340 from microbiomedata/2339-release-nmdc-schema-version-v1140
Generate release artifacts for `nmdc-schema` version `v11.4.0`
2 parents 99fec8c + beb5281 commit c622217

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‎nmdc_schema/nmdc-pydantic.py

Lines changed: 12 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -740,6 +740,8 @@ class BiosampleCategoryEnum(str, Enum):
740740
Department_of_Energy_Office_of_Science_Biological_and_Environmental_Research_Program_Laboratory_Science_Focus_Areas = "SFA"
741741
Facilities_Integrating_Collaborations_for_User_Science = "FICUS"
742742
National_Science_FoundationAPOSTROPHEs_National_Ecological_Observatory_Network = "NEON"
743+
# Bioenergy Research Centers funded by the Biological Systems Science Division of the U.S. Department of Energy's Biological and Environmental Research Program.
744+
Bioenergy_Research_Centers = "BRC"
743745

744746

745747
class SubstanceRoleEnum(str, Enum):
@@ -2200,6 +2202,8 @@ class FileTypeEnum(str, Enum):
22002202
Direct_Infusion_FT_ICR_MS_Raw_Data = "Direct Infusion FT ICR-MS Raw Data"
22012203
# Liquid chromatographically separated MS1 and Data-Dependent MS2 binary instrument file
22022204
LC_DDA_MSSOLIDUSMS_Raw_Data = "LC-DDA-MS/MS Raw Data"
2205+
# Gas chromatography-mass spectrometry raw data, full scan mode.
2206+
GC_MS_Raw_Data = "GC-MS Raw Data"
22032207
# A configuration toml file used by various programs to store settings that are specific to their respective software.
22042208
Configuration_toml = "Configuration toml"
22052209
# LC-MS-based lipidomics analysis results table
@@ -2552,9 +2556,6 @@ class Database(ConfiguredBaseModel):
25522556
processed_sample_set: Optional[List[ProcessedSample]] = Field(None, description="""This property links a database object to the set of processed samples within it.""", json_schema_extra = { "linkml_meta": {'alias': 'processed_sample_set',
25532557
'domain_of': ['Database'],
25542558
'mixins': ['object_set']} })
2555-
protocol_execution_set: Optional[List[ProtocolExecution]] = Field(None, description="""This property links a database object to the set of protocol executions within it.""", json_schema_extra = { "linkml_meta": {'alias': 'protocol_execution_set',
2556-
'domain_of': ['Database'],
2557-
'mixins': ['object_set']} })
25582559
storage_process_set: Optional[List[StorageProcess]] = Field(None, description="""This property links a database object to the set of storage processes within it.""", json_schema_extra = { "linkml_meta": {'alias': 'storage_process_set',
25592560
'domain_of': ['Database'],
25602561
'mixins': ['object_set']} })
@@ -11922,6 +11923,8 @@ class ProtocolExecution(PlannedProcess):
1192211923
A PlannedProces that has PlannedProcess parts. Can be used to represent the case of someone following a Protocol.
1192311924
"""
1192411925
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'class_uri': 'nmdc:ProtocolExecution',
11926+
'deprecated': 'not used, not fulfilling intended purpose '
11927+
'https://github.com/microbiomedata/nmdc-schema/issues/2336',
1192511928
'from_schema': 'https://w3id.org/nmdc/nmdc',
1192611929
'slot_usage': {'has_input': {'name': 'has_input',
1192711930
'pattern': '^(nmdc):(bsm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$',
@@ -11947,11 +11950,16 @@ class ProtocolExecution(PlannedProcess):
1194711950
'syntax': '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'}}}})
1194811951

1194911952
has_process_parts: List[str] = Field(..., description="""The MaterialProcessing steps that are discrete parts of the ProtocolExecution.""", json_schema_extra = { "linkml_meta": {'alias': 'has_process_parts',
11953+
'deprecated': 'not used '
11954+
'https://github.com/microbiomedata/nmdc-schema/issues/2336',
1195011955
'domain_of': ['ProtocolExecution'],
1195111956
'list_elements_ordered': True,
1195211957
'structured_pattern': {'interpolated': True,
1195311958
'syntax': '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'}} })
11954-
protocol_execution_category: ProtocolCategoryEnum = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'protocol_execution_category', 'domain_of': ['ProtocolExecution']} })
11959+
protocol_execution_category: ProtocolCategoryEnum = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'protocol_execution_category',
11960+
'deprecated': 'not used '
11961+
'https://github.com/microbiomedata/nmdc-schema/issues/2336',
11962+
'domain_of': ['ProtocolExecution']} })
1195511963
has_input: Optional[List[str]] = Field(None, description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input',
1195611964
'aliases': ['input'],
1195711965
'domain_of': ['PlannedProcess'],

‎nmdc_schema/nmdc.py

Lines changed: 9 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Auto generated from nmdc.yaml by pythongen.py version: 0.0.1
2-
# Generation date: 2025-01-30T16:05:51
2+
# Generation date: 2025-02-12T08:47:56
33
# Schema: NMDC
44
#
55
# id: https://w3id.org/nmdc/nmdc
@@ -511,7 +511,6 @@ class Database(YAMLRoot):
511511
manifest_set: Optional[Union[Dict[Union[str, ManifestId], Union[dict, "Manifest"]], List[Union[dict, "Manifest"]]]] = empty_dict()
512512
material_processing_set: Optional[Union[Dict[Union[str, MaterialProcessingId], Union[dict, "MaterialProcessing"]], List[Union[dict, "MaterialProcessing"]]]] = empty_dict()
513513
processed_sample_set: Optional[Union[Dict[Union[str, ProcessedSampleId], Union[dict, "ProcessedSample"]], List[Union[dict, "ProcessedSample"]]]] = empty_dict()
514-
protocol_execution_set: Optional[Union[Dict[Union[str, ProtocolExecutionId], Union[dict, "ProtocolExecution"]], List[Union[dict, "ProtocolExecution"]]]] = empty_dict()
515514
storage_process_set: Optional[Union[Dict[Union[str, StorageProcessId], Union[dict, "StorageProcess"]], List[Union[dict, "StorageProcess"]]]] = empty_dict()
516515
study_set: Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]] = empty_dict()
517516
workflow_execution_set: Optional[Union[Dict[Union[str, WorkflowExecutionId], Union[dict, "WorkflowExecution"]], List[Union[dict, "WorkflowExecution"]]]] = empty_dict()
@@ -551,8 +550,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
551550

552551
self._normalize_inlined_as_list(slot_name="processed_sample_set", slot_type=ProcessedSample, key_name="id", keyed=True)
553552

554-
self._normalize_inlined_as_list(slot_name="protocol_execution_set", slot_type=ProtocolExecution, key_name="id", keyed=True)
555-
556553
self._normalize_inlined_as_list(slot_name="storage_process_set", slot_type=StorageProcess, key_name="id", keyed=True)
557554

558555
self._normalize_inlined_as_list(slot_name="study_set", slot_type=Study, key_name="id", keyed=True)
@@ -6932,6 +6929,10 @@ class BiosampleCategoryEnum(EnumDefinitionImpl):
69326929
NEON = PermissibleValue(
69336930
text="NEON",
69346931
meaning=None)
6932+
BRC = PermissibleValue(
6933+
text="BRC",
6934+
description="""Bioenergy Research Centers funded by the Biological Systems Science Division of the U.S. Department of Energy's Biological and Environmental Research Program.""",
6935+
meaning=None)
69356936

69366937
_defn = EnumDefinition(
69376938
name="BiosampleCategoryEnum",
@@ -7688,6 +7689,10 @@ def _addvals(cls):
76887689
PermissibleValue(
76897690
text="LC-DDA-MS/MS Raw Data",
76907691
description="Liquid chromatographically separated MS1 and Data-Dependent MS2 binary instrument file"))
7692+
setattr(cls, "GC-MS Raw Data",
7693+
PermissibleValue(
7694+
text="GC-MS Raw Data",
7695+
description="Gas chromatography-mass spectrometry raw data, full scan mode."))
76917696
setattr(cls, "Configuration toml",
76927697
PermissibleValue(
76937698
text="Configuration toml",

‎nmdc_schema/nmdc.schema.json

Lines changed: 3 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -5441,7 +5441,8 @@
54415441
"SIP",
54425442
"SFA",
54435443
"FICUS",
5444-
"NEON"
5444+
"NEON",
5445+
"BRC"
54455446
],
54465447
"title": "BiosampleCategoryEnum",
54475448
"type": "string"
@@ -6870,16 +6871,6 @@
68706871
"null"
68716872
]
68726873
},
6873-
"protocol_execution_set": {
6874-
"description": "This property links a database object to the set of protocol executions within it.",
6875-
"items": {
6876-
"$ref": "#/$defs/ProtocolExecution"
6877-
},
6878-
"type": [
6879-
"array",
6880-
"null"
6881-
]
6882-
},
68836874
"storage_process_set": {
68846875
"description": "This property links a database object to the set of storage processes within it.",
68856876
"items": {
@@ -8016,6 +8007,7 @@
80168007
"Annotation Statistics",
80178008
"Direct Infusion FT ICR-MS Raw Data",
80188009
"LC-DDA-MS/MS Raw Data",
8010+
"GC-MS Raw Data",
80198011
"Configuration toml",
80208012
"LC-MS Lipidomics Results",
80218013
"LC-MS Lipidomics Processed Data",
@@ -15750,16 +15742,6 @@
1575015742
"null"
1575115743
]
1575215744
},
15753-
"protocol_execution_set": {
15754-
"description": "This property links a database object to the set of protocol executions within it.",
15755-
"items": {
15756-
"$ref": "#/$defs/ProtocolExecution"
15757-
},
15758-
"type": [
15759-
"array",
15760-
"null"
15761-
]
15762-
},
1576315745
"storage_process_set": {
1576415746
"description": "This property links a database object to the set of storage processes within it.",
1576515747
"items": {

‎nmdc_schema/nmdc_materialized_patterns.schema.json

Lines changed: 3 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -5443,7 +5443,8 @@
54435443
"SIP",
54445444
"SFA",
54455445
"FICUS",
5446-
"NEON"
5446+
"NEON",
5447+
"BRC"
54475448
],
54485449
"title": "BiosampleCategoryEnum",
54495450
"type": "string"
@@ -6881,16 +6882,6 @@
68816882
"null"
68826883
]
68836884
},
6884-
"protocol_execution_set": {
6885-
"description": "This property links a database object to the set of protocol executions within it.",
6886-
"items": {
6887-
"$ref": "#/$defs/ProtocolExecution"
6888-
},
6889-
"type": [
6890-
"array",
6891-
"null"
6892-
]
6893-
},
68946885
"storage_process_set": {
68956886
"description": "This property links a database object to the set of storage processes within it.",
68966887
"items": {
@@ -8032,6 +8023,7 @@
80328023
"Annotation Statistics",
80338024
"Direct Infusion FT ICR-MS Raw Data",
80348025
"LC-DDA-MS/MS Raw Data",
8026+
"GC-MS Raw Data",
80358027
"Configuration toml",
80368028
"LC-MS Lipidomics Results",
80378029
"LC-MS Lipidomics Processed Data",
@@ -15831,16 +15823,6 @@
1583115823
"null"
1583215824
]
1583315825
},
15834-
"protocol_execution_set": {
15835-
"description": "This property links a database object to the set of protocol executions within it.",
15836-
"items": {
15837-
"$ref": "#/$defs/ProtocolExecution"
15838-
},
15839-
"type": [
15840-
"array",
15841-
"null"
15842-
]
15843-
},
1584415826
"storage_process_set": {
1584515827
"description": "This property links a database object to the set of storage processes within it.",
1584615828
"items": {

‎nmdc_schema/nmdc_materialized_patterns.yaml

Lines changed: 14 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1018,6 +1018,13 @@ enums:
10181018
text: NEON
10191019
meaning: https://www.neonscience.org
10201020
title: National Science Foundation's National Ecological Observatory Network
1021+
BRC:
1022+
text: BRC
1023+
description: Bioenergy Research Centers funded by the Biological Systems Science
1024+
Division of the U.S. Department of Energy's Biological and Environmental
1025+
Research Program.
1026+
meaning: https://www.genomicscience.energy.gov/bioenergy-research-centers/
1027+
title: Bioenergy Research Centers
10211028
SubstanceRoleEnum:
10221029
name: SubstanceRoleEnum
10231030
from_schema: https://w3id.org/nmdc/nmdc
@@ -4201,6 +4208,9 @@ enums:
42014208
text: LC-DDA-MS/MS Raw Data
42024209
description: Liquid chromatographically separated MS1 and Data-Dependent MS2
42034210
binary instrument file
4211+
GC-MS Raw Data:
4212+
text: GC-MS Raw Data
4213+
description: Gas chromatography-mass spectrometry raw data, full scan mode.
42044214
Configuration toml:
42054215
text: Configuration toml
42064216
description: A configuration toml file used by various programs to store settings
@@ -4975,6 +4985,7 @@ slots:
49754985
name: protocol_execution_set
49764986
description: This property links a database object to the set of protocol executions
49774987
within it.
4988+
deprecated: not used https://github.com/microbiomedata/nmdc-schema/issues/2336
49784989
from_schema: https://w3id.org/nmdc/nmdc
49794990
mixins:
49804991
- object_set
@@ -5034,12 +5045,14 @@ slots:
50345045
range: QuantityValue
50355046
protocol_execution_category:
50365047
name: protocol_execution_category
5048+
deprecated: not used https://github.com/microbiomedata/nmdc-schema/issues/2336
50375049
from_schema: https://w3id.org/nmdc/nmdc
50385050
range: ProtocolCategoryEnum
50395051
required: true
50405052
has_process_parts:
50415053
name: has_process_parts
50425054
description: A list of process parts that make up a protocol.
5055+
deprecated: not used https://github.com/microbiomedata/nmdc-schema/issues/2336
50435056
from_schema: https://w3id.org/nmdc/nmdc
50445057
list_elements_ordered: true
50455058
range: PlannedProcess
@@ -19478,7 +19491,6 @@ classes:
1947819491
- manifest_set
1947919492
- material_processing_set
1948019493
- processed_sample_set
19481-
- protocol_execution_set
1948219494
- storage_process_set
1948319495
- study_set
1948419496
- workflow_execution_set
@@ -19641,6 +19653,7 @@ classes:
1964119653
name: ProtocolExecution
1964219654
description: A PlannedProces that has PlannedProcess parts. Can be used to represent
1964319655
the case of someone following a Protocol.
19656+
deprecated: not used, not fulfilling intended purpose https://github.com/microbiomedata/nmdc-schema/issues/2336
1964419657
from_schema: https://w3id.org/nmdc/nmdc
1964519658
is_a: PlannedProcess
1964619659
slots:

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