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Try to remove some duplication at the model level #165

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a100314
Move creator types to common schema, unify across formats
jmchilton Mar 25, 2026
061f812
Fix JSON-LD predicate collisions in schema-salad codegen
jmchilton Mar 24, 2026
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4 changes: 2 additions & 2 deletions gxformat2/normalized/_conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,9 +58,9 @@
WorkflowStepOutput,
WorkflowStepType,
)
from ..schema.native import CreatorOrganization as NativeCreatorOrganization
from ..schema.native import CreatorPerson as NativeCreatorPerson
from ..schema.native import (
NativeCreatorOrganization,
NativeCreatorPerson,
NativeGalaxyWorkflow,
NativeInputConnection,
NativePostJobAction,
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8 changes: 4 additions & 4 deletions gxformat2/normalized/_native.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,8 @@
from gxformat2.schema.native import (
_discriminate_comments,
_discriminate_creator,
NativeCreatorOrganization,
NativeCreatorPerson,
CreatorOrganization,
CreatorPerson,
NativeFrameComment,
NativeFreehandComment,
NativeGalaxyWorkflow,
Expand Down Expand Up @@ -53,8 +53,8 @@

NativeCreator: TypeAlias = Annotated[
Union[
Annotated[NativeCreatorPerson, Tag("NativeCreatorPerson")],
Annotated[NativeCreatorOrganization, Tag("NativeCreatorOrganization")],
Annotated[CreatorPerson, Tag("CreatorPerson")],
Annotated[CreatorOrganization, Tag("CreatorOrganization")],
],
Discriminator(_discriminate_creator),
]
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80 changes: 40 additions & 40 deletions gxformat2/schema/gxformat2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,6 +186,43 @@ class ToolShedRepository(BaseModel):
owner: str = Field(description="The owner of the tool shed repository this tool can be found in.")
tool_shed: str = Field(description="The URI of the tool shed containing the repository this tool can be found in - typically this should be toolshed.g2.bx.psu.edu.")

class BaseCreator(BaseModel):
"""Base fields shared by all creator types, corresponding to schema.org
Thing properties common to both Person and Organization."""

model_config = ConfigDict(populate_by_name=True, extra="allow")

name: None | str = Field(default=None, description="Full name of the person or organization.")
identifier: None | str = Field(default=None, description="Persistent identifier, typically an ORCID URL (e.g. ``https://orcid.org/0000-0001-2345-6789``) or bare ORCID.")
url: None | str = Field(default=None, description="Website or profile URL.")
email: None | str = Field(default=None, description="Email address. May include a ``mailto:`` prefix.")
image: None | str = Field(default=None, description="URL to an image or avatar.")
address: None | str = Field(default=None, description="Physical or mailing address.")
alternateName: None | str = Field(default=None, description="An alternate name or alias.")
telephone: None | str = Field(default=None, description="Telephone number.")
faxNumber: None | str = Field(default=None, description="Fax number.")

class CreatorPerson(BaseCreator):
"""A person who created or contributed to the workflow.
Corresponds to a `schema.org Person <https://schema.org/Person>`_."""

model_config = ConfigDict(populate_by_name=True, extra="allow")

class_: Literal["Person"] = Field(default="Person", alias="class", description="Creator type discriminator (``Person``).")
givenName: None | str = Field(default=None, description="Given (first) name.")
familyName: None | str = Field(default=None, description="Family (last) name.")
honorificPrefix: None | str = Field(default=None, description="Honorific prefix (e.g. ``Dr``, ``Prof``).")
honorificSuffix: None | str = Field(default=None, description="Honorific suffix (e.g. ``M.D.``, ``PhD``).")
jobTitle: None | str = Field(default=None, description="Job title or role.")

class CreatorOrganization(BaseCreator):
"""An organization that created or contributed to the workflow.
Corresponds to a `schema.org Organization <https://schema.org/Organization>`_."""

model_config = ConfigDict(populate_by_name=True, extra="allow")

class_: Literal["Organization"] = Field(default="Organization", alias="class", description="Creator type discriminator (``Organization``).")

class WorkflowInputParameter(InputParameter, HasStepPosition):
model_config = ConfigDict(populate_by_name=True, extra="allow")

Expand Down Expand Up @@ -327,43 +364,6 @@ class FreehandComment(BaseComment):
thickness: None | float | int = Field(default=None, description="Line thickness.")
line: list[list[float]] | None = Field(default=None, description="Array of ``[x, y]`` coordinate pairs defining the freehand line path.")

class BaseCreator(BaseModel):
"""Base fields shared by all creator types, corresponding to schema.org
Thing properties common to both Person and Organization."""

model_config = ConfigDict(populate_by_name=True, extra="allow")

name: None | str = Field(default=None, description="Full name of the person or organization.")
identifier: None | str = Field(default=None, description="Persistent identifier, typically an ORCID URL (e.g. ``https://orcid.org/0000-0001-2345-6789``) or bare ORCID.")
url: None | str = Field(default=None, description="Website or profile URL.")
email: None | str = Field(default=None, description="Email address. May include a ``mailto:`` prefix.")
image: None | str = Field(default=None, description="URL to an image or avatar.")
address: None | str = Field(default=None, description="Physical or mailing address.")
alternateName: None | str = Field(default=None, description="An alternate name or alias.")
telephone: None | str = Field(default=None, description="Telephone number.")
faxNumber: None | str = Field(default=None, description="Fax number.")

class CreatorPerson(BaseCreator):
"""A person who created or contributed to the workflow.
Corresponds to a `schema.org Person <https://schema.org/Person>`_."""

model_config = ConfigDict(populate_by_name=True, extra="allow")

class_: Literal["Person"] = Field(default="Person", alias="class", description="Creator type discriminator (``Person``).")
givenName: None | str = Field(default=None, description="Given (first) name.")
familyName: None | str = Field(default=None, description="Family (last) name.")
honorificPrefix: None | str = Field(default=None, description="Honorific prefix (e.g. ``Dr``, ``Prof``).")
honorificSuffix: None | str = Field(default=None, description="Honorific suffix (e.g. ``M.D.``, ``PhD``).")
jobTitle: None | str = Field(default=None, description="Job title or role.")

class CreatorOrganization(BaseCreator):
"""An organization that created or contributed to the workflow.
Corresponds to a `schema.org Organization <https://schema.org/Organization>`_."""

model_config = ConfigDict(populate_by_name=True, extra="allow")

class_: Literal["Organization"] = Field(default="Organization", alias="class", description="Creator type discriminator (``Organization``).")

class GalaxyWorkflow(Process, HasUUID):
"""A Galaxy workflow description. This record corresponds to the description of a workflow that should be executable
on a Galaxy server that includes the contained tool definitions.
Expand Down Expand Up @@ -410,6 +410,9 @@ class GalaxyWorkflow(Process, HasUUID):
StepPosition.model_rebuild()
ReferencesTool.model_rebuild()
ToolShedRepository.model_rebuild()
BaseCreator.model_rebuild()
CreatorPerson.model_rebuild()
CreatorOrganization.model_rebuild()
WorkflowInputParameter.model_rebuild()
WorkflowOutputParameter.model_rebuild()
WorkflowStep.model_rebuild()
Expand All @@ -422,9 +425,6 @@ class GalaxyWorkflow(Process, HasUUID):
MarkdownComment.model_rebuild()
FrameComment.model_rebuild()
FreehandComment.model_rebuild()
BaseCreator.model_rebuild()
CreatorPerson.model_rebuild()
CreatorOrganization.model_rebuild()
GalaxyWorkflow.model_rebuild()


Expand Down
80 changes: 40 additions & 40 deletions gxformat2/schema/gxformat2_strict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,6 +186,43 @@ class ToolShedRepository(BaseModel):
owner: str = Field(description="The owner of the tool shed repository this tool can be found in.")
tool_shed: str = Field(description="The URI of the tool shed containing the repository this tool can be found in - typically this should be toolshed.g2.bx.psu.edu.")

class BaseCreator(BaseModel):
"""Base fields shared by all creator types, corresponding to schema.org
Thing properties common to both Person and Organization."""

model_config = ConfigDict(populate_by_name=True, extra="forbid")

name: None | str = Field(default=None, description="Full name of the person or organization.")
identifier: None | str = Field(default=None, description="Persistent identifier, typically an ORCID URL (e.g. ``https://orcid.org/0000-0001-2345-6789``) or bare ORCID.")
url: None | str = Field(default=None, description="Website or profile URL.")
email: None | str = Field(default=None, description="Email address. May include a ``mailto:`` prefix.")
image: None | str = Field(default=None, description="URL to an image or avatar.")
address: None | str = Field(default=None, description="Physical or mailing address.")
alternateName: None | str = Field(default=None, description="An alternate name or alias.")
telephone: None | str = Field(default=None, description="Telephone number.")
faxNumber: None | str = Field(default=None, description="Fax number.")

class CreatorPerson(BaseCreator):
"""A person who created or contributed to the workflow.
Corresponds to a `schema.org Person <https://schema.org/Person>`_."""

model_config = ConfigDict(populate_by_name=True, extra="forbid")

class_: Literal["Person"] = Field(default="Person", alias="class", description="Creator type discriminator (``Person``).")
givenName: None | str = Field(default=None, description="Given (first) name.")
familyName: None | str = Field(default=None, description="Family (last) name.")
honorificPrefix: None | str = Field(default=None, description="Honorific prefix (e.g. ``Dr``, ``Prof``).")
honorificSuffix: None | str = Field(default=None, description="Honorific suffix (e.g. ``M.D.``, ``PhD``).")
jobTitle: None | str = Field(default=None, description="Job title or role.")

class CreatorOrganization(BaseCreator):
"""An organization that created or contributed to the workflow.
Corresponds to a `schema.org Organization <https://schema.org/Organization>`_."""

model_config = ConfigDict(populate_by_name=True, extra="forbid")

class_: Literal["Organization"] = Field(default="Organization", alias="class", description="Creator type discriminator (``Organization``).")

class WorkflowInputParameter(InputParameter, HasStepPosition):
model_config = ConfigDict(populate_by_name=True, extra="forbid")

Expand Down Expand Up @@ -327,43 +364,6 @@ class FreehandComment(BaseComment):
thickness: None | float | int = Field(default=None, description="Line thickness.")
line: list[list[float]] | None = Field(default=None, description="Array of ``[x, y]`` coordinate pairs defining the freehand line path.")

class BaseCreator(BaseModel):
"""Base fields shared by all creator types, corresponding to schema.org
Thing properties common to both Person and Organization."""

model_config = ConfigDict(populate_by_name=True, extra="forbid")

name: None | str = Field(default=None, description="Full name of the person or organization.")
identifier: None | str = Field(default=None, description="Persistent identifier, typically an ORCID URL (e.g. ``https://orcid.org/0000-0001-2345-6789``) or bare ORCID.")
url: None | str = Field(default=None, description="Website or profile URL.")
email: None | str = Field(default=None, description="Email address. May include a ``mailto:`` prefix.")
image: None | str = Field(default=None, description="URL to an image or avatar.")
address: None | str = Field(default=None, description="Physical or mailing address.")
alternateName: None | str = Field(default=None, description="An alternate name or alias.")
telephone: None | str = Field(default=None, description="Telephone number.")
faxNumber: None | str = Field(default=None, description="Fax number.")

class CreatorPerson(BaseCreator):
"""A person who created or contributed to the workflow.
Corresponds to a `schema.org Person <https://schema.org/Person>`_."""

model_config = ConfigDict(populate_by_name=True, extra="forbid")

class_: Literal["Person"] = Field(default="Person", alias="class", description="Creator type discriminator (``Person``).")
givenName: None | str = Field(default=None, description="Given (first) name.")
familyName: None | str = Field(default=None, description="Family (last) name.")
honorificPrefix: None | str = Field(default=None, description="Honorific prefix (e.g. ``Dr``, ``Prof``).")
honorificSuffix: None | str = Field(default=None, description="Honorific suffix (e.g. ``M.D.``, ``PhD``).")
jobTitle: None | str = Field(default=None, description="Job title or role.")

class CreatorOrganization(BaseCreator):
"""An organization that created or contributed to the workflow.
Corresponds to a `schema.org Organization <https://schema.org/Organization>`_."""

model_config = ConfigDict(populate_by_name=True, extra="forbid")

class_: Literal["Organization"] = Field(default="Organization", alias="class", description="Creator type discriminator (``Organization``).")

class GalaxyWorkflow(Process, HasUUID):
"""A Galaxy workflow description. This record corresponds to the description of a workflow that should be executable
on a Galaxy server that includes the contained tool definitions.
Expand Down Expand Up @@ -410,6 +410,9 @@ class GalaxyWorkflow(Process, HasUUID):
StepPosition.model_rebuild()
ReferencesTool.model_rebuild()
ToolShedRepository.model_rebuild()
BaseCreator.model_rebuild()
CreatorPerson.model_rebuild()
CreatorOrganization.model_rebuild()
WorkflowInputParameter.model_rebuild()
WorkflowOutputParameter.model_rebuild()
WorkflowStep.model_rebuild()
Expand All @@ -422,9 +425,6 @@ class GalaxyWorkflow(Process, HasUUID):
MarkdownComment.model_rebuild()
FrameComment.model_rebuild()
FreehandComment.model_rebuild()
BaseCreator.model_rebuild()
CreatorPerson.model_rebuild()
CreatorOrganization.model_rebuild()
GalaxyWorkflow.model_rebuild()


Expand Down
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