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10.6.0
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@pkalita-lbl
pkalita-lbl committed Jul 19, 2024
1 parent 60f913d commit 3e43038
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Showing 4 changed files with 594 additions and 322 deletions.
108 changes: 88 additions & 20 deletions nmdc_schema/nmdc.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Auto generated from nmdc.yaml by pythongen.py version: 0.0.1
# Generation date: 2024-06-21T09:39:03
# Generation date: 2024-07-19T10:42:33
# Schema: NMDC
#
# id: https://w3id.org/nmdc/nmdc
Expand Down Expand Up @@ -298,7 +298,7 @@ class MetatranscriptomeAnnotationActivityId(WorkflowExecutionActivityId):
pass


class MetatranscriptomeActivityId(WorkflowExecutionActivityId):
class MetatranscriptomeExpressionAnalysisId(WorkflowExecutionActivityId):
pass


Expand Down Expand Up @@ -414,7 +414,9 @@ class Database(YAMLRoot):
metagenome_assembly_set: Optional[Union[Dict[Union[str, MetagenomeAssemblyId], Union[dict, "MetagenomeAssembly"]], List[Union[dict, "MetagenomeAssembly"]]]] = empty_dict()
metagenome_sequencing_activity_set: Optional[Union[Dict[Union[str, MetagenomeSequencingActivityId], Union[dict, "MetagenomeSequencingActivity"]], List[Union[dict, "MetagenomeSequencingActivity"]]]] = empty_dict()
metaproteomics_analysis_activity_set: Optional[Union[Dict[Union[str, MetaproteomicsAnalysisActivityId], Union[dict, "MetaproteomicsAnalysisActivity"]], List[Union[dict, "MetaproteomicsAnalysisActivity"]]]] = empty_dict()
metatranscriptome_activity_set: Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]] = empty_dict()
metatranscriptome_annotation_set: Optional[Union[Dict[Union[str, MetatranscriptomeAnnotationActivityId], Union[dict, "MetatranscriptomeAnnotationActivity"]], List[Union[dict, "MetatranscriptomeAnnotationActivity"]]]] = empty_dict()
metatranscriptome_assembly_set: Optional[Union[Dict[Union[str, MetatranscriptomeAssemblyId], Union[dict, "MetatranscriptomeAssembly"]], List[Union[dict, "MetatranscriptomeAssembly"]]]] = empty_dict()
metatranscriptome_expression_analysis_set: Optional[Union[Dict[Union[str, MetatranscriptomeExpressionAnalysisId], Union[dict, "MetatranscriptomeExpressionAnalysis"]], List[Union[dict, "MetatranscriptomeExpressionAnalysis"]]]] = empty_dict()
nom_analysis_activity_set: Optional[Union[Dict[Union[str, NomAnalysisActivityId], Union[dict, "NomAnalysisActivity"]], List[Union[dict, "NomAnalysisActivity"]]]] = empty_dict()
omics_processing_set: Optional[Union[Dict[Union[str, OmicsProcessingId], Union[dict, "OmicsProcessing"]], List[Union[dict, "OmicsProcessing"]]]] = empty_dict()
planned_process_set: Optional[Union[Dict[Union[str, PlannedProcessId], Union[dict, "PlannedProcess"]], List[Union[dict, "PlannedProcess"]]]] = empty_dict()
Expand Down Expand Up @@ -461,7 +463,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):

self._normalize_inlined_as_list(slot_name="metaproteomics_analysis_activity_set", slot_type=MetaproteomicsAnalysisActivity, key_name="id", keyed=True)

self._normalize_inlined_as_list(slot_name="metatranscriptome_activity_set", slot_type=MetatranscriptomeActivity, key_name="id", keyed=True)
self._normalize_inlined_as_list(slot_name="metatranscriptome_annotation_set", slot_type=MetatranscriptomeAnnotationActivity, key_name="id", keyed=True)

self._normalize_inlined_as_list(slot_name="metatranscriptome_assembly_set", slot_type=MetatranscriptomeAssembly, key_name="id", keyed=True)

self._normalize_inlined_as_list(slot_name="metatranscriptome_expression_analysis_set", slot_type=MetatranscriptomeExpressionAnalysis, key_name="id", keyed=True)

self._normalize_inlined_as_list(slot_name="nom_analysis_activity_set", slot_type=NomAnalysisActivity, key_name="id", keyed=True)

Expand Down Expand Up @@ -4007,6 +4013,8 @@ class LibraryPreparation(BiosampleProcessing):
library_preparation_kit: Optional[str] = None
library_type: Optional[Union[str, "LibraryTypeEnum"]] = None
pcr_cycles: Optional[int] = None
is_stranded: Optional[Union[bool, Bool]] = None
stranded_orientation: Optional[Union[str, "StrandedOrientationEnum"]] = None

def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self._is_empty(self.id):
Expand Down Expand Up @@ -4035,6 +4043,12 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self.pcr_cycles is not None and not isinstance(self.pcr_cycles, int):
self.pcr_cycles = int(self.pcr_cycles)

if self.is_stranded is not None and not isinstance(self.is_stranded, Bool):
self.is_stranded = Bool(self.is_stranded)

if self.stranded_orientation is not None and not isinstance(self.stranded_orientation, StrandedOrientationEnum):
self.stranded_orientation = StrandedOrientationEnum(self.stranded_orientation)

super().__post_init__(**kwargs)
self.designated_class = str(self.class_class_curie)

Expand Down Expand Up @@ -5600,18 +5614,18 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):


@dataclass
class MetatranscriptomeActivity(WorkflowExecutionActivity):
class MetatranscriptomeExpressionAnalysis(WorkflowExecutionActivity):
"""
A metatranscriptome activity that e.g. pools assembly and annotation activity.
A workflow process that provides expression values and read counts for gene features predicted on the contigs.
"""
_inherited_slots: ClassVar[List[str]] = []

class_class_uri: ClassVar[URIRef] = NMDC["MetatranscriptomeActivity"]
class_class_curie: ClassVar[str] = "nmdc:MetatranscriptomeActivity"
class_name: ClassVar[str] = "MetatranscriptomeActivity"
class_model_uri: ClassVar[URIRef] = NMDC.MetatranscriptomeActivity
class_class_uri: ClassVar[URIRef] = NMDC["MetatranscriptomeExpressionAnalysis"]
class_class_curie: ClassVar[str] = "nmdc:MetatranscriptomeExpressionAnalysis"
class_name: ClassVar[str] = "MetatranscriptomeExpressionAnalysis"
class_model_uri: ClassVar[URIRef] = NMDC.MetatranscriptomeExpressionAnalysis

id: Union[str, MetatranscriptomeActivityId] = None
id: Union[str, MetatranscriptomeExpressionAnalysisId] = None
execution_resource: str = None
git_url: str = None
has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None
Expand All @@ -5622,8 +5636,8 @@ class MetatranscriptomeActivity(WorkflowExecutionActivity):
def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
if self._is_empty(self.id):
self.MissingRequiredField("id")
if not isinstance(self.id, MetatranscriptomeActivityId):
self.id = MetatranscriptomeActivityId(self.id)
if not isinstance(self.id, MetatranscriptomeExpressionAnalysisId):
self.id = MetatranscriptomeExpressionAnalysisId(self.id)

if self.type is not None and not isinstance(self.type, str):
self.type = str(self.type)
Expand Down Expand Up @@ -5923,6 +5937,26 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):


# Enumerations
class StrandedOrientationEnum(EnumDefinitionImpl):
"""
This enumeration specifies information about stranded RNA library preparations.
"""
_defn = EnumDefinition(
name="StrandedOrientationEnum",
description="This enumeration specifies information about stranded RNA library preparations.",
)

@classmethod
def _addvals(cls):
setattr(cls, "antisense orientation",
PermissibleValue(
text="antisense orientation",
description="Orientation that is complementary (non-coding) to a sequence of messenger RNA."))
setattr(cls, "sense orientation",
PermissibleValue(
text="sense orientation",
description="Orientation that corresponds to the coding sequence of messenger RNA."))

class InstrumentModelEnum(EnumDefinitionImpl):

Orbitrap = PermissibleValue(text="Orbitrap")
Expand Down Expand Up @@ -6327,6 +6361,22 @@ def _addvals(cls):
PermissibleValue(
text="LC-DDA-MS/MS Raw Data",
description="Liquid chromatographically separated MS1 and Data-Dependent MS2 binary instrument file"))
setattr(cls, "Metatranscriptome Expression",
PermissibleValue(
text="Metatranscriptome Expression",
description="""Metatranscriptome expression values and read counts for gene features predicted on contigs"""))
setattr(cls, "Metatranscriptome Expression Intergenic",
PermissibleValue(
text="Metatranscriptome Expression Intergenic",
description="Metatranscriptome expression values and read counts for intergenic regions."))
setattr(cls, "Metatranscriptome Expression Info File",
PermissibleValue(
text="Metatranscriptome Expression Info File",
description="File containing version information on the expression workflow"))
setattr(cls, "rRNA Filtered Sequencing Reads",
PermissibleValue(
text="rRNA Filtered Sequencing Reads",
description="File containing ribosomal reads from the read qc filtering step."))

class CreditEnum(EnumDefinitionImpl):

Expand Down Expand Up @@ -6517,9 +6567,15 @@ class FailureWhereEnum(EnumDefinitionImpl):
MetagenomeAssembly = PermissibleValue(
text="MetagenomeAssembly",
description="A failure has occurred in metagenome assembly, a workflow process.")
MetatranscriptomeActivity = PermissibleValue(
text="MetatranscriptomeActivity",
description="A failure has occurred in metatranscriptome analysis, a workflow process.")
MetatranscriptomeExpressionAnalysis = PermissibleValue(
text="MetatranscriptomeExpressionAnalysis",
description="A failure has occurred in metatranscriptome expression analysis, a workflow process.")
MetatranscriptomeAnnotation = PermissibleValue(
text="MetatranscriptomeAnnotation",
description="A failure has occurred in metatranscriptome annotation analysis, a workflow process.")
MetatranscriptomeAssembly = PermissibleValue(
text="MetatranscriptomeAssembly",
description="A failure has occurred in metatranscriptome assembly analysis, a workflow process.")
MagsAnalysisActivity = PermissibleValue(
text="MagsAnalysisActivity",
description="""A failure has occurred in binning, a workflow process to generate metagenome-assembled genomes (MAGS).""")
Expand Down Expand Up @@ -8747,6 +8803,12 @@ class slots:
slots.pcr_cycles = Slot(uri=NMDC.pcr_cycles, name="pcr_cycles", curie=NMDC.curie('pcr_cycles'),
model_uri=NMDC.pcr_cycles, domain=None, range=Optional[int])

slots.is_stranded = Slot(uri=NMDC.is_stranded, name="is_stranded", curie=NMDC.curie('is_stranded'),
model_uri=NMDC.is_stranded, domain=None, range=Optional[Union[bool, Bool]])

slots.stranded_orientation = Slot(uri=NMDC.stranded_orientation, name="stranded_orientation", curie=NMDC.curie('stranded_orientation'),
model_uri=NMDC.stranded_orientation, domain=None, range=Optional[Union[str, "StrandedOrientationEnum"]])

slots.mass = Slot(uri=NMDC.mass, name="mass", curie=NMDC.curie('mass'),
model_uri=NMDC.mass, domain=None, range=Optional[Union[dict, QuantityValue]])

Expand Down Expand Up @@ -8867,8 +8929,8 @@ class slots:
slots.metagenome_sequencing_activity_set = Slot(uri=NMDC.metagenome_sequencing_activity_set, name="metagenome_sequencing_activity_set", curie=NMDC.curie('metagenome_sequencing_activity_set'),
model_uri=NMDC.metagenome_sequencing_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetagenomeSequencingActivityId], Union[dict, "MetagenomeSequencingActivity"]], List[Union[dict, "MetagenomeSequencingActivity"]]]])

slots.metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'),
model_uri=NMDC.metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]])
slots.metatranscriptome_expression_analysis_set = Slot(uri=NMDC.metatranscriptome_expression_analysis_set, name="metatranscriptome_expression_analysis_set", curie=NMDC.curie('metatranscriptome_expression_analysis_set'),
model_uri=NMDC.metatranscriptome_expression_analysis_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeExpressionAnalysisId], Union[dict, "MetatranscriptomeExpressionAnalysis"]], List[Union[dict, "MetatranscriptomeExpressionAnalysis"]]]])

slots.read_qc_analysis_activity_set = Slot(uri=NMDC.read_qc_analysis_activity_set, name="read_qc_analysis_activity_set", curie=NMDC.curie('read_qc_analysis_activity_set'),
model_uri=NMDC.read_qc_analysis_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, ReadQcAnalysisActivityId], Union[dict, "ReadQcAnalysisActivity"]], List[Union[dict, "ReadQcAnalysisActivity"]]]])
Expand All @@ -8894,6 +8956,12 @@ class slots:
slots.library_preparation_set = Slot(uri=NMDC.library_preparation_set, name="library_preparation_set", curie=NMDC.curie('library_preparation_set'),
model_uri=NMDC.library_preparation_set, domain=Database, range=Optional[Union[Dict[Union[str, LibraryPreparationId], Union[dict, "LibraryPreparation"]], List[Union[dict, "LibraryPreparation"]]]])

slots.metatranscriptome_assembly_set = Slot(uri=NMDC.metatranscriptome_assembly_set, name="metatranscriptome_assembly_set", curie=NMDC.curie('metatranscriptome_assembly_set'),
model_uri=NMDC.metatranscriptome_assembly_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeAssemblyId], Union[dict, "MetatranscriptomeAssembly"]], List[Union[dict, "MetatranscriptomeAssembly"]]]])

slots.metatranscriptome_annotation_set = Slot(uri=NMDC.metatranscriptome_annotation_set, name="metatranscriptome_annotation_set", curie=NMDC.curie('metatranscriptome_annotation_set'),
model_uri=NMDC.metatranscriptome_annotation_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeAnnotationActivityId], Union[dict, "MetatranscriptomeAnnotationActivity"]], List[Union[dict, "MetatranscriptomeAnnotationActivity"]]]])

slots.omics_type = Slot(uri=NMDC.omics_type, name="omics_type", curie=NMDC.curie('omics_type'),
model_uri=NMDC.omics_type, domain=OmicsProcessing, range=Optional[Union[dict, "ControlledTermValue"]])

Expand Down Expand Up @@ -11725,8 +11793,8 @@ class slots:
model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId],
pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))

slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'),
model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId],
slots.MetatranscriptomeExpressionAnalysis_id = Slot(uri=NMDC.id, name="MetatranscriptomeExpressionAnalysis_id", curie=NMDC.curie('id'),
model_uri=NMDC.MetatranscriptomeExpressionAnalysis_id, domain=MetatranscriptomeExpressionAnalysis, range=Union[str, MetatranscriptomeExpressionAnalysisId],
pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))

slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'),
Expand Down
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