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fix: add default= to schema_version_bump.py #1157

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merged 4 commits into from
Nov 12, 2024
Merged

fix: add default= to schema_version_bump.py #1157

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85db9d1
fix: add default= to schema_version_bump.py
dbirman Nov 12, 2024
91da948
fix: add default into files
dbirman Nov 12, 2024
1bce88b
tests: fix test to match default= pattern
dbirman Nov 12, 2024
238b6b6
chore: lint
dbirman Nov 12, 2024
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/acquisition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ class Acquisition(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/acquisition.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.0.3"]] = Field("1.0.3")
schema_version: SkipValidation[Literal["1.0.3"]] = Field(default="1.0.3")
protocol_id: List[str] = Field(default=[], title="Protocol ID", description="DOI for protocols.io")
experimenter_full_name: List[str] = Field(
...,
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/data_description.py
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Expand Up @@ -40,7 +40,7 @@ class DataDescription(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/data_description.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.0.3"]] = Field("1.0.3")
schema_version: SkipValidation[Literal["1.0.3"]] = Field(default="1.0.3")
license: Literal["CC-BY-4.0"] = Field("CC-BY-4.0", title="License")

platform: Platform.ONE_OF = Field(
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/instrument.py
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Expand Up @@ -35,7 +35,7 @@ class Instrument(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/instrument.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.0.3"]] = Field("1.0.3")
schema_version: SkipValidation[Literal["1.0.3"]] = Field(default="1.0.3")

instrument_id: Optional[str] = Field(
default=None,
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/metadata.py
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Expand Up @@ -71,7 +71,7 @@ class Metadata(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/metadata.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.1.1"]] = Field("1.1.1")
schema_version: SkipValidation[Literal["1.1.1"]] = Field(default="1.1.1")
id: UUID = Field(
default_factory=uuid4,
alias="_id",
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/procedures.py
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Expand Up @@ -649,7 +649,7 @@ class Procedures(AindCoreModel):
_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/procedures.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})

schema_version: SkipValidation[Literal["1.1.3"]] = Field("1.1.3")
schema_version: SkipValidation[Literal["1.1.3"]] = Field(default="1.1.3")
subject_id: str = Field(
...,
description="Unique identifier for the subject. If this is not a Allen LAS ID, indicate this in the Notes.",
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/processing.py
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Expand Up @@ -124,7 +124,7 @@ class Processing(AindCoreModel):

_DESCRIBED_BY_URL: str = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/processing.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.1.3"]] = Field("1.1.3")
schema_version: SkipValidation[Literal["1.1.3"]] = Field(default="1.1.3")

processing_pipeline: PipelineProcess = Field(
..., description="Pipeline used to process data", title="Processing Pipeline"
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/quality_control.py
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Expand Up @@ -174,7 +174,7 @@ class QualityControl(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/quality_control.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.2.1"]] = Field("1.2.1")
schema_version: SkipValidation[Literal["1.2.1"]] = Field(default="1.2.1")
evaluations: List[QCEvaluation] = Field(..., title="Evaluations")
notes: Optional[str] = Field(default=None, title="Notes")

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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/rig.py
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Expand Up @@ -51,7 +51,7 @@ class Rig(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/rig.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.0.3"]] = Field("1.0.3")
schema_version: SkipValidation[Literal["1.0.3"]] = Field(default="1.0.3")
rig_id: str = Field(
...,
description="Unique rig identifier, name convention: <room>-<apparatus name>-<date modified YYYYMMDD>",
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/session.py
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Expand Up @@ -534,7 +534,7 @@ class Session(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/session.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.0.3"]] = Field("1.0.3")
schema_version: SkipValidation[Literal["1.0.3"]] = Field(default="1.0.3")
protocol_id: List[str] = Field(default=[], title="Protocol ID", description="DOI for protocols.io")
experimenter_full_name: List[str] = Field(
...,
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2 changes: 1 addition & 1 deletion src/aind_data_schema/core/subject.py
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Expand Up @@ -89,7 +89,7 @@ class Subject(AindCoreModel):

_DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/subject.py"
describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
schema_version: SkipValidation[Literal["1.0.2"]] = Field("1.0.2")
schema_version: SkipValidation[Literal["1.0.2"]] = Field(default="1.0.2")
subject_id: str = Field(
...,
description="Unique identifier for the subject. If this is not a Allen LAS ID, indicate this in the Notes.",
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4 changes: 3 additions & 1 deletion src/aind_data_schema/utils/schema_version_bump.py
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Expand Up @@ -102,7 +102,9 @@ def _get_updated_file(python_file_path: str, new_ver: str) -> list:
file_lines = f.readlines()
for line in file_lines:
if "schema_version: SkipValidation[Literal[" in str(line):
new_line_str = f' schema_version: SkipValidation[Literal["{new_ver}"]] = Field("{new_ver}")\n'
new_line_str = (
f' schema_version: SkipValidation[Literal["{new_ver}"]] = Field(default="{new_ver}")\n'
)
new_line = new_line_str.encode()
else:
new_line = line
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4 changes: 2 additions & 2 deletions tests/test_bump_schema_versions.py
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Expand Up @@ -77,10 +77,10 @@ def test_update_files(self, mock_write: MagicMock):
handler._update_files({Subject: new_subject_version, Session: new_session_version})

expected_line_change0 = (
f'schema_version: SkipValidation[Literal["{new_subject_version}"]] = Field("{new_subject_version}")'
f'schema_version: SkipValidation[Literal["{new_subject_version}"]] = Field(default="{new_subject_version}")'
)
expected_line_change1 = (
f'schema_version: SkipValidation[Literal["{new_session_version}"]] = Field("{new_session_version}")'
f'schema_version: SkipValidation[Literal["{new_session_version}"]] = Field(default="{new_session_version}")'
)

mock_write_args0 = mock_write.mock_calls[0].args
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