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Merge pull request #2703 from microbiomedata/2702-release-nmdc-schema-version-11130
Generate release artifacts for `nmdc-schema` version `11.13.0`
2 parents 01315da + 40e9680 commit 332447f

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-3702
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‎Dockerfile‎

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# Use Python 3.9 because that's the Python version listed in `pyproject.toml`.
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FROM python:3.9
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FROM python:3.10
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WORKDIR /nmdc-schema
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# Install jq.
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RUN apt-get update && \
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apt-get install -y jq
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# Download and install yq.
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# Reference: https://github.com/mikefarah/yq#install
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RUN wget https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 -O /usr/bin/yq && \

‎docker-compose.yml‎

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version: '3'
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services:
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app:
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# Use the container image built from the specified Dockerfile;

nmdc_schema/migrators/migrator_from_11_11_0_to_11_12_2.py renamed to nmdc_schema/migrators/migrator_from_11_11_0_to_11_13_0.py

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from nmdc_schema.migrators.migrator_base import MigratorBase
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from nmdc_schema.migrators.partials.migrator_from_11_11_0_to_11_12_2 import (
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from nmdc_schema.migrators.partials.migrator_from_11_11_0_to_11_13_0 import (
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get_migrator_classes,
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)
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@@ -10,7 +10,7 @@ class Migrator(MigratorBase):
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"""
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_from_version = "11.11.0"
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_to_version = "11.12.2"
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_to_version = "11.13.0"
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def upgrade(self, commit_changes: bool = False) -> None:
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r"""

nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_12_2/__init__.py renamed to nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0/__init__.py

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@@ -1,10 +1,10 @@
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from typing import List, Type
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from nmdc_schema.migrators.migrator_base import MigratorBase
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from nmdc_schema.migrators.partials.migrator_from_11_11_0_to_11_12_2 import (
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migrator_from_11_11_0_to_11_12_2_part_1,
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migrator_from_11_11_0_to_11_12_2_part_2,
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migrator_from_11_11_0_to_11_12_2_part_3
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from nmdc_schema.migrators.partials.migrator_from_11_11_0_to_11_13_0 import (
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migrator_from_11_11_0_to_11_13_0_part_1,
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migrator_from_11_11_0_to_11_13_0_part_2,
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migrator_from_11_11_0_to_11_13_0_part_3
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)
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"""
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return [
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migrator_from_11_11_0_to_11_12_2_part_1.Migrator,
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migrator_from_11_11_0_to_11_12_2_part_2.Migrator,
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migrator_from_11_11_0_to_11_12_2_part_3.Migrator
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migrator_from_11_11_0_to_11_13_0_part_1.Migrator,
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migrator_from_11_11_0_to_11_13_0_part_2.Migrator,
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migrator_from_11_11_0_to_11_13_0_part_3.Migrator
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]

nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_12_2/migrator_from_11_11_0_to_11_12_2_part_1.py renamed to nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0/migrator_from_11_11_0_to_11_13_0_part_1.py

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@@ -13,7 +13,7 @@ class Migrator(MigratorBase):
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'''
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_from_version = '11.11.0'
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_to_version = '11.12.2.part_1'
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_to_version = '11.13.0.part_1'
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def upgrade(self, commit_changes: bool = False) -> None:
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r'''

nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_12_2/migrator_from_11_11_0_to_11_12_2_part_2.py renamed to nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0/migrator_from_11_11_0_to_11_13_0_part_2.py

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r"""A check-only migrator that raises an exception if any QuantityValue's has_unit slot
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is not valid against the slot's storage_unit or UnitEnum constraints."""
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_from_version = '11.12.2.part_1'
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_to_version = '11.12.2.part_2'
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_from_version = '11.13.0.part_1'
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_to_version = '11.13.0.part_2'
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def __init__(self, *args, **kwargs):
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super().__init__(*args, **kwargs)

nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_12_2/migrator_from_11_11_0_to_11_12_2_part_3.py renamed to nmdc_schema/migrators/partials/migrator_from_11_11_0_to_11_13_0/migrator_from_11_11_0_to_11_13_0_part_3.py

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@@ -6,10 +6,10 @@ class Migrator(MigratorBase):
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Migrates a database between two schemas.
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"""
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_from_version = "11.12.2.part_2"
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_to_version = "11.12.2.part_3"
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_from_version = "11.13.0.part_2"
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_to_version = "11.13.0.part_3"
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def upgrade(self) -> None:
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def upgrade(self, commit_changes: bool = False) -> None:
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r"""
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Migrates the database from conforming to the original schema, to conforming to the new schema.
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"""
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True
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"""
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prefix = "igsn:"
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igsn_values = []
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igsn_values = biosample.get("igsn_biosample_identifiers")
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igsn_values = biosample.get("igsn_biosample_identifiers", [])
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biosample_id = biosample.get("id")
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for record in igsn_values:
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if not record.startswith(prefix):

‎nmdc_schema/nmdc-pydantic.py‎

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‎nmdc_schema/nmdc.py‎

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