From b8b6cfef7bd3b00f3cf99246ca28ffd5ebcdc287 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 20:48:30 +0100
Subject: [PATCH 01/13] wip
---
pyproject.toml | 2 +-
stac_extension_genmeta/core.py | 6 +++---
stac_extension_genmeta/testing.py | 12 +++++++-----
3 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 9169482..c49f38f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,7 +30,7 @@ genmeta_cli = "stac_extension_genmeta.cli:app"
packages = ["stac_extension_genmeta"]
[project.optional-dependencies]
-validation = ["requests", "pystac[validation]"]
+test = ["requests", "pystac[validation]", "difflib"]
[tool.setuptools.dynamic]
version = { attr = "stac_extension_genmeta.__version__" }
diff --git a/stac_extension_genmeta/core.py b/stac_extension_genmeta/core.py
index c8b1eb2..15ace43 100644
--- a/stac_extension_genmeta/core.py
+++ b/stac_extension_genmeta/core.py
@@ -12,7 +12,7 @@ from .schema import generate_schema
import json
-class BaseExtensionModel(BaseException):
+class BaseExtensionModel(BaseModel):
"""Base class for extensions models."""
model_config = ConfigDict(populate_by_name=True)
@@ -59,7 +59,7 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
# If not possible, self.md is set to `None`
props = {
key: self._get_property(info.alias, str)
- for key, info in model_cls.__fields__.items()
+ for key, info in model_cls.model_fields.items()
}
props = {p: v for p, v in props.items() if v is not None}
self.md = model_cls(**props) if props else None
@@ -81,7 +81,7 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
# Set properties
md = md or model_cls(**kwargs)
for key, value in md.model_dump(exclude_unset=True).items():
- alias = model_cls.__fields__[key].alias or key
+ alias = model_cls.model_fields[key].alias or key
self._set_property(alias, value, pop_if_none=False)
@classmethod
diff --git a/stac_extension_genmeta/testing.py b/stac_extension_genmeta/testing.py
index 5f51e2d..f134f7c 100644
--- a/stac_extension_genmeta/testing.py
+++ b/stac_extension_genmeta/testing.py
@@ -2,6 +2,8 @@ import pystac
from datetime import datetime
import random
import json
+import requests
+import difflib
def create_dummy_item(date=None):
@@ -65,9 +67,11 @@ def basic_test(
validate: bool = True
):
print(
- f"Extension metadata model: \n{ext_md.__class__.schema_json(indent=2)}"
+ f"Extension metadata model: \n{ext_md.__class__.model_json_schema()}"
)
+ ext_cls.print_schema()
+
def apply(stac_obj, method="arg"):
"""
Apply the extension to the item
@@ -81,7 +85,7 @@ def basic_test(
elif method == "dict":
d = {
name: getattr(ext_md, name)
- for name in ext_md.__fields__
+ for name in ext_md.model_fields
}
print(f"Passing kwargs: {d}")
ext.apply(**d)
@@ -97,7 +101,7 @@ def basic_test(
Compare the metadata carried by the stac object with the expected metadata.
"""
read_ext = ext_cls(stac_obj)
- for field in ext_md.__class__.__fields__:
+ for field in ext_md.__class__.model_fields:
ref = getattr(ext_md, field)
got = getattr(read_ext, field)
assert got == ref, f"'{field}': values differ: {got} (expected {ref})"
@@ -152,7 +156,6 @@ def basic_test(
def is_schema_url_synced(cls):
- import requests
local_schema = cls.get_schema()
url = cls.get_schema_uri()
remote_schema = requests.get(url).json()
@@ -165,7 +168,6 @@ def is_schema_url_synced(cls):
)
if local_schema != remote_schema:
print("Schema differs:")
- import difflib
def _json2str(dic):
return json.dumps(dic, indent=2).split("\n")
--
GitLab
From 5c4b39091f8740388670eb812ecdcc704e0f8c06 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 21:01:18 +0100
Subject: [PATCH 02/13] wip
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4bb2302..4a210d4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,6 +16,6 @@ Tests:
except: [main, tags]
script:
- pip install pip --upgrade
- - pip install .
+ - pip install .[test]
- python3 tests/extensions_test.py
--
GitLab
From 34a3ad94cfc689088467d70e65724625fec0e12b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 21:06:08 +0100
Subject: [PATCH 03/13] wip
---
pyproject.toml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyproject.toml b/pyproject.toml
index c49f38f..105cdbd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,7 +30,7 @@ genmeta_cli = "stac_extension_genmeta.cli:app"
packages = ["stac_extension_genmeta"]
[project.optional-dependencies]
-test = ["requests", "pystac[validation]", "difflib"]
+test = ["requests", "pystac[validation]"]
[tool.setuptools.dynamic]
version = { attr = "stac_extension_genmeta.__version__" }
--
GitLab
From 9a9de7816d0f4b2adf53ab95e0eecc08ad98b1f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 21:06:57 +0100
Subject: [PATCH 04/13] wip
---
stac_extension_genmeta/__init__.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/stac_extension_genmeta/__init__.py b/stac_extension_genmeta/__init__.py
index ff56c03..55989ae 100644
--- a/stac_extension_genmeta/__init__.py
+++ b/stac_extension_genmeta/__init__.py
@@ -2,4 +2,4 @@
from .core import create_extension_cls, BaseExtensionModel # noqa
-__version__ = "0.1.3"
+__version__ = "0.1.3-dev1"
--
GitLab
From 4c176b89a6a2db947c2ccae388814c6603177baf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 21:46:50 +0100
Subject: [PATCH 05/13] wip
---
stac_extension_genmeta/__init__.py | 2 +-
stac_extension_genmeta/testing.py | 61 ++++++++++++++----------------
2 files changed, 29 insertions(+), 34 deletions(-)
diff --git a/stac_extension_genmeta/__init__.py b/stac_extension_genmeta/__init__.py
index 55989ae..9e7c95b 100644
--- a/stac_extension_genmeta/__init__.py
+++ b/stac_extension_genmeta/__init__.py
@@ -2,4 +2,4 @@
from .core import create_extension_cls, BaseExtensionModel # noqa
-__version__ = "0.1.3-dev1"
+__version__ = "0.1.3-dev2"
diff --git a/stac_extension_genmeta/testing.py b/stac_extension_genmeta/testing.py
index f134f7c..29623d8 100644
--- a/stac_extension_genmeta/testing.py
+++ b/stac_extension_genmeta/testing.py
@@ -1,3 +1,5 @@
+"""Testing module."""
+import os
import pystac
from datetime import datetime
import random
@@ -17,21 +19,19 @@ def create_dummy_item(date=None):
geom = {
"type": "Polygon",
"coordinates": [
- [[4.032730583418401, 43.547450099338604],
- [4.036414917971517, 43.75162726634343],
- [3.698685718905037, 43.75431706444037],
- [3.6962018175925073, 43.55012996681564],
- [4.032730583418401, 43.547450099338604]]
- ]
+ [
+ [4.032730583418401, 43.547450099338604],
+ [4.036414917971517, 43.75162726634343],
+ [3.698685718905037, 43.75431706444037],
+ [3.6962018175925073, 43.55012996681564],
+ [4.032730583418401, 43.547450099338604],
+ ]
+ ],
}
- asset = pystac.Asset(
- href="https://example.com/SP67_FR_subset_1.tif"
- )
+ asset = pystac.Asset(href="https://example.com/SP67_FR_subset_1.tif")
val = f"item_{random.uniform(10000, 80000)}"
spat_extent = pystac.SpatialExtent([[0, 0, 2, 3]])
- temp_extent = pystac.TemporalExtent(
- intervals=[(None, None)]
- )
+ temp_extent = pystac.TemporalExtent(intervals=[(None, None)])
item = pystac.Item(
id=val,
@@ -41,7 +41,7 @@ def create_dummy_item(date=None):
properties={},
assets={"ndvi": asset},
href="https://example.com/collections/collection-test3/items/{val}",
- collection="collection-test3"
+ collection="collection-test3",
)
col = pystac.Collection(
@@ -59,16 +59,14 @@ METHODS = ["arg", "md", "dict"]
def basic_test(
- ext_md,
- ext_cls,
- item_test: bool = True,
- asset_test: bool = True,
- collection_test: bool = True,
- validate: bool = True
+ ext_md,
+ ext_cls,
+ item_test: bool = True,
+ asset_test: bool = True,
+ collection_test: bool = True,
+ validate: bool = True,
):
- print(
- f"Extension metadata model: \n{ext_md.__class__.model_json_schema()}"
- )
+ print(f"Extension metadata model: \n{ext_md.__class__.model_json_schema()}")
ext_cls.print_schema()
@@ -83,10 +81,7 @@ def basic_test(
elif method == "md":
ext.apply(md=ext_md)
elif method == "dict":
- d = {
- name: getattr(ext_md, name)
- for name in ext_md.model_fields
- }
+ d = {name: getattr(ext_md, name) for name in ext_md.model_fields}
print(f"Passing kwargs: {d}")
ext.apply(**d)
@@ -155,9 +150,13 @@ def basic_test(
test_collection(method)
+CI_COMMIT_REF_NAME = os.environ.get("CI_COMMIT_REF_NAME")
+
+
def is_schema_url_synced(cls):
local_schema = cls.get_schema()
url = cls.get_schema_uri()
+ url = url.replace("/-/raw/main/", f"/-/raw/{CI_COMMIT_REF_NAME}/") if CI_COMMIT_REF_NAME else url
remote_schema = requests.get(url).json()
print(
f"Local schema is :\n"
@@ -168,14 +167,10 @@ def is_schema_url_synced(cls):
)
if local_schema != remote_schema:
print("Schema differs:")
+
def _json2str(dic):
return json.dumps(dic, indent=2).split("\n")
- diff = difflib.unified_diff(
- _json2str(local_schema),
- _json2str(remote_schema)
- )
+ diff = difflib.unified_diff(_json2str(local_schema), _json2str(remote_schema))
print("\n".join(diff))
- raise ValueError(
- f"Please update the schema located in {url}"
- )
+ raise ValueError(f"Please update the schema located in {url}")
--
GitLab
From 3aaf8fde682937d4bfd328f3fd656db37dacb533 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 22:34:42 +0100
Subject: [PATCH 06/13] wip
---
.gitlab-ci.yml | 21 +--------------
.gitlab/ci/base.yml | 23 ++++++++++++++++
LICENSE | 2 +-
pyproject.toml | 7 ++---
stac_extension_genmeta/__init__.py | 2 +-
stac_extension_genmeta/testing.py | 5 +++-
tests/extensions_test.py | 42 +++++++++++++-----------------
7 files changed, 50 insertions(+), 52 deletions(-)
create mode 100644 .gitlab/ci/base.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4a210d4..de9b93d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,21 +1,2 @@
include:
- - project: "cdos-pub/pycode-quality"
- ref: "main"
- file:
- - ".gitlab/ci/static-analysis.yml"
- - ".gitlab/ci/pip.yml"
-
-stages:
- - Static Analysis
- - Test
- - Pip
-
-Tests:
- image: "registry.forgemia.inra.fr/cdos-pub/pycode-quality/python-venv:3.10"
- stage: Test
- except: [main, tags]
- script:
- - pip install pip --upgrade
- - pip install .[test]
- - python3 tests/extensions_test.py
-
+ - ".gitlab/ci/base.yml"
diff --git a/.gitlab/ci/base.yml b/.gitlab/ci/base.yml
new file mode 100644
index 0000000..bff0450
--- /dev/null
+++ b/.gitlab/ci/base.yml
@@ -0,0 +1,23 @@
+include:
+ - project: "cdos-pub/pycode-quality"
+ ref: "main"
+ file:
+ - ".gitlab/ci/static-analysis.yml"
+ - ".gitlab/ci/pip.yml"
+
+variables:
+ PIP_EXTRA_INDEX_URL: https://forgemia.inra.fr/api/v4/projects/10919/packages/pypi/simple
+ PACKAGE_INSTALL_EXTRAS: "[test]"
+
+stages:
+ - Static Analysis
+ - Test
+ - Pip
+
+Tests:
+ extends: .static_analysis_with_pip_install
+ stage: Test
+ allow_failure: false
+ script:
+ - pytest tests/
+
diff --git a/LICENSE b/LICENSE
index a6b5cd4..6c258c1 100644
--- a/LICENSE
+++ b/LICENSE
@@ -186,7 +186,7 @@
same "printed page" as the copyright notice for easier
identification within third-party archives.
- Copyright 2024 INRAE
+ Copyright 2024-2025 INRAE
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
diff --git a/pyproject.toml b/pyproject.toml
index 105cdbd..fa832e3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ description = "Helper to build custom STAC extensions based on pydantic models"
authors = [
{ name = "Rémi Cresson", email = "remi.cresson@inrae.fr" },
]
-requires-python = ">=3.7"
+requires-python = ">=3.8"
dependencies = [
"pydantic >= 2.0.0",
"pystac",
@@ -23,14 +23,11 @@ classifiers = [
"Operating System :: OS Independent",
]
-[project.scripts]
-genmeta_cli = "stac_extension_genmeta.cli:app"
-
[tool.setuptools]
packages = ["stac_extension_genmeta"]
[project.optional-dependencies]
-test = ["requests", "pystac[validation]"]
+test = ["requests", "pystac[validation]", "pytest"]
[tool.setuptools.dynamic]
version = { attr = "stac_extension_genmeta.__version__" }
diff --git a/stac_extension_genmeta/__init__.py b/stac_extension_genmeta/__init__.py
index 9e7c95b..9c021c3 100644
--- a/stac_extension_genmeta/__init__.py
+++ b/stac_extension_genmeta/__init__.py
@@ -2,4 +2,4 @@
from .core import create_extension_cls, BaseExtensionModel # noqa
-__version__ = "0.1.3-dev2"
+__version__ = "0.1.3-dev3"
diff --git a/stac_extension_genmeta/testing.py b/stac_extension_genmeta/testing.py
index 29623d8..47c0d32 100644
--- a/stac_extension_genmeta/testing.py
+++ b/stac_extension_genmeta/testing.py
@@ -1,4 +1,5 @@
"""Testing module."""
+
import os
import pystac
from datetime import datetime
@@ -156,7 +157,9 @@ CI_COMMIT_REF_NAME = os.environ.get("CI_COMMIT_REF_NAME")
def is_schema_url_synced(cls):
local_schema = cls.get_schema()
url = cls.get_schema_uri()
- url = url.replace("/-/raw/main/", f"/-/raw/{CI_COMMIT_REF_NAME}/") if CI_COMMIT_REF_NAME else url
+ url = (
+ url.replace("/-/raw/main/", f"/-/raw/{CI_COMMIT_REF_NAME}/") if CI_COMMIT_REF_NAME else url
+ )
remote_schema = requests.get(url).json()
print(
f"Local schema is :\n"
diff --git a/tests/extensions_test.py b/tests/extensions_test.py
index 85ec701..0172862 100644
--- a/tests/extensions_test.py
+++ b/tests/extensions_test.py
@@ -1,38 +1,32 @@
-from stac_extension_genmeta import create_extension_cls
+from stac_extension_genmeta import create_extension_cls, BaseExtensionModel
from stac_extension_genmeta.testing import basic_test
-from pydantic import BaseModel, Field, ConfigDict
-from typing import List
+from pydantic import Field
+from typing import List, Final
# Extension parameters
-SCHEMA_URI: str = "https://example.com/image-process/v1.0.0/schema.json"
-PREFIX: str = "some_prefix"
+SCHEMA_URI: Final = "https://example.com/image-process/v1.0.0/schema.json"
+PREFIX: Final = "some_prefix:"
+NAME: Final = PREFIX + "name"
+AUTHORS: Final = PREFIX + "authors"
+VERSION: Final = PREFIX + "version"
-# Extension metadata model
-class MyExtensionMetadataModel(BaseModel):
- # Required so that one model can be instantiated with the attribute name
- # rather than the alias
- model_config = ConfigDict(populate_by_name=True)
+class MyExtensionMetadataModel(BaseExtensionModel):
+ """Extension metadata model."""
- # Metadata fields
- name: str = Field(title="Process name", alias=f"{PREFIX}:name")
- authors: List[str] = Field(title="Authors", alias=f"{PREFIX}:authors")
- version: str = Field(title="Process version", alias=f"{PREFIX}:version")
- opt_field: str | None = Field(title="Some optional field", alias=f"{PREFIX}:opt_field", default=None)
+ name: str = Field(title="Process name", alias=NAME)
+ authors: List[str] = Field(title="Authors", alias=AUTHORS)
+ version: str = Field(title="Process version", alias=VERSION)
+ opt_field: str | None = Field(
+ title="Some optional field", alias=f"{PREFIX}:opt_field", default=None
+ )
# Create the extension class
-MyExtension = create_extension_cls(
- model_cls=MyExtensionMetadataModel,
- schema_uri=SCHEMA_URI
-)
+MyExtension = create_extension_cls(model_cls=MyExtensionMetadataModel, schema_uri=SCHEMA_URI)
# Metadata fields
-ext_md = MyExtensionMetadataModel(
- name="test",
- authors=["michel", "denis"],
- version="alpha"
-)
+ext_md = MyExtensionMetadataModel(name="test", authors=["michel", "denis"], version="alpha")
basic_test(ext_md, MyExtension, validate=False)
--
GitLab
From d41540eedeeed5b4d16ce8930c270e638e838fe9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 22:40:52 +0100
Subject: [PATCH 07/13] wip
---
stac_extension_genmeta/core.py | 22 ++++++++++++++++------
stac_extension_genmeta/schema.py | 1 +
tests/extensions_test.py | 15 ++++++++-------
3 files changed, 25 insertions(+), 13 deletions(-)
diff --git a/stac_extension_genmeta/core.py b/stac_extension_genmeta/core.py
index 15ace43..ce5f35a 100644
--- a/stac_extension_genmeta/core.py
+++ b/stac_extension_genmeta/core.py
@@ -1,6 +1,4 @@
-"""
-Processing extension
-"""
+"""Generic metadata creation."""
from typing import Any, Generic, TypeVar, Union, cast
from pystac.extensions.base import PropertiesExtension, ExtensionManagementMixin
@@ -19,8 +17,7 @@ class BaseExtensionModel(BaseModel):
def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExtension:
- """
- This method creates a pystac extension from a pydantic model.
+ """This method creates a pystac extension from a pydantic model.
Args:
model_cls: pydantic model class
@@ -45,7 +42,9 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
PropertiesExtension,
ExtensionManagementMixin[Union[pystac.Item, pystac.Collection]],
):
+ """Custom extension class."""
def __init__(self, obj: T):
+ """Initializer."""
if isinstance(obj, pystac.Item):
self.properties = obj.properties
elif isinstance(obj, (pystac.Asset, pystac.Collection)):
@@ -65,10 +64,11 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
self.md = model_cls(**props) if props else None
def __getattr__(self, item):
- # forward getattr to self.md
+ """forward getattr to self.md."""
return getattr(self.md, item) if self.md else None
def apply(self, md: model_cls = None, **kwargs) -> None:
+ """Apply the metadata."""
if md is None and not kwargs:
raise ValueError("At least `md` or kwargs is required")
@@ -86,10 +86,12 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
@classmethod
def get_schema_uri(cls) -> str:
+ """Get schema URI."""
return schema_uri
@classmethod
def get_schema(cls) -> dict:
+ """Get schema as dict."""
return generate_schema(
model_cls=model_cls,
title=f"STAC extension from {model_cls.__name__} model",
@@ -99,6 +101,7 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
@classmethod
def print_schema(cls):
+ """Print schema."""
print(
"\033[92mPlease copy/paste the schema below in the right place "
f"in the repository so it can be accessed from \033[94m"
@@ -107,11 +110,13 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
@classmethod
def export_schema(cls, json_file):
+ """Export schema."""
with open(json_file, "w") as f:
json.dump(cls.get_schema(), f, indent=2)
@classmethod
def ext(cls, obj: T, add_if_missing: bool = False) -> model_cls.__name__:
+ """Create the extension."""
if isinstance(obj, pystac.Item):
cls.ensure_has_extension(obj, add_if_missing)
return cast(CustomExtension[T], ItemCustomExtension(obj))
@@ -126,23 +131,28 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
)
class ItemCustomExtension(CustomExtension[pystac.Item]):
+ """Item custom extension."""
pass
class AssetCustomExtension(CustomExtension[pystac.Asset]):
+ """Asset custom extension."""
asset_href: str
properties: dict[str, Any]
additional_read_properties: Iterable[dict[str, Any]] | None = None
def __init__(self, asset: pystac.Asset):
+ """Initializer."""
self.asset_href = asset.href
self.properties = asset.extra_fields
if asset.owner and isinstance(asset.owner, pystac.Item):
self.additional_read_properties = [asset.owner.properties]
class CollectionCustomExtension(CustomExtension[pystac.Collection]):
+ """Collection curstom extension."""
properties: dict[str, Any]
def __init__(self, collection: pystac.Collection):
+ """Initializer."""
self.properties = collection.extra_fields
CustomExtension.__name__ = f"CustomExtensionFrom{model_cls.__name__}"
diff --git a/stac_extension_genmeta/schema.py b/stac_extension_genmeta/schema.py
index ffe1cd7..53c6c57 100644
--- a/stac_extension_genmeta/schema.py
+++ b/stac_extension_genmeta/schema.py
@@ -7,6 +7,7 @@ def generate_schema(
description: str,
schema_uri: str
) -> dict:
+ """Generate the schema."""
properties = model_cls.model_json_schema()
# prune "required"
properties.pop("required", None)
diff --git a/tests/extensions_test.py b/tests/extensions_test.py
index 0172862..71480f0 100644
--- a/tests/extensions_test.py
+++ b/tests/extensions_test.py
@@ -1,3 +1,5 @@
+"""Tests example."""
+
from stac_extension_genmeta import create_extension_cls, BaseExtensionModel
from stac_extension_genmeta.testing import basic_test
from pydantic import Field
@@ -22,12 +24,11 @@ class MyExtensionMetadataModel(BaseExtensionModel):
)
-# Create the extension class
-MyExtension = create_extension_cls(model_cls=MyExtensionMetadataModel, schema_uri=SCHEMA_URI)
-
-# Metadata fields
-ext_md = MyExtensionMetadataModel(name="test", authors=["michel", "denis"], version="alpha")
+def test_example():
+ # Create the extension class
+ MyExtension = create_extension_cls(model_cls=MyExtensionMetadataModel, schema_uri=SCHEMA_URI)
-basic_test(ext_md, MyExtension, validate=False)
+ # Metadata fields
+ ext_md = MyExtensionMetadataModel(name="test", authors=["michel", "denis"], version="alpha")
-MyExtension.print_schema()
+ basic_test(ext_md, MyExtension, validate=False)
--
GitLab
From 49532ac556c3800316dd6b1fee100ce96a7eb79f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 22:44:27 +0100
Subject: [PATCH 08/13] wip
---
stac_extension_genmeta/testing.py | 27 +++++++++------------------
tests/extensions_test.py | 7 ++-----
2 files changed, 11 insertions(+), 23 deletions(-)
diff --git a/stac_extension_genmeta/testing.py b/stac_extension_genmeta/testing.py
index 47c0d32..40f8619 100644
--- a/stac_extension_genmeta/testing.py
+++ b/stac_extension_genmeta/testing.py
@@ -10,6 +10,7 @@ import difflib
def create_dummy_item(date=None):
+ """Create dummy item."""
if not date:
date = datetime.now().replace(year=1999)
@@ -67,14 +68,13 @@ def basic_test(
collection_test: bool = True,
validate: bool = True,
):
+ """Perform the basic testing of the extension class."""
print(f"Extension metadata model: \n{ext_md.__class__.model_json_schema()}")
ext_cls.print_schema()
def apply(stac_obj, method="arg"):
- """
- Apply the extension to the item
- """
+ """Apply the extension to the item."""
print(f"Check extension applied to {stac_obj.__class__.__name__}")
ext = ext_cls.ext(stac_obj, add_if_missing=True)
if method == "arg":
@@ -87,15 +87,11 @@ def basic_test(
ext.apply(**d)
def print_item(item):
- """
- Print item as JSON
- """
+ """Print item as JSON."""
print(json.dumps(item.to_dict(), indent=2))
def comp(stac_obj):
- """
- Compare the metadata carried by the stac object with the expected metadata.
- """
+ """Compare the metadata carried by the stac object with the expected metadata."""
read_ext = ext_cls(stac_obj)
for field in ext_md.__class__.model_fields:
ref = getattr(ext_md, field)
@@ -103,9 +99,7 @@ def basic_test(
assert got == ref, f"'{field}': values differ: {got} (expected {ref})"
def test_item(method):
- """
- Test extension against item
- """
+ """Test extension against item."""
item, _ = create_dummy_item()
apply(item, method)
print_item(item)
@@ -115,9 +109,7 @@ def basic_test(
comp(item)
def test_asset(method):
- """
- Test extension against asset
- """
+ """Test extension against asset."""
item, _ = create_dummy_item()
apply(item.assets["ndvi"], method)
print_item(item)
@@ -127,9 +119,7 @@ def basic_test(
comp(item.assets["ndvi"])
def test_collection(method):
- """
- Test extension against collection
- """
+ """Test extension against collection."""
item, col = create_dummy_item()
print_item(col)
apply(col, method)
@@ -155,6 +145,7 @@ CI_COMMIT_REF_NAME = os.environ.get("CI_COMMIT_REF_NAME")
def is_schema_url_synced(cls):
+ """Check if the schema is in sync with the repository."""
local_schema = cls.get_schema()
url = cls.get_schema_uri()
url = (
diff --git a/tests/extensions_test.py b/tests/extensions_test.py
index 71480f0..8e19920 100644
--- a/tests/extensions_test.py
+++ b/tests/extensions_test.py
@@ -14,7 +14,7 @@ VERSION: Final = PREFIX + "version"
class MyExtensionMetadataModel(BaseExtensionModel):
- """Extension metadata model."""
+ """Extension metadata model example."""
name: str = Field(title="Process name", alias=NAME)
authors: List[str] = Field(title="Authors", alias=AUTHORS)
@@ -25,10 +25,7 @@ class MyExtensionMetadataModel(BaseExtensionModel):
def test_example():
- # Create the extension class
+ """Test example function."""
MyExtension = create_extension_cls(model_cls=MyExtensionMetadataModel, schema_uri=SCHEMA_URI)
-
- # Metadata fields
ext_md = MyExtensionMetadataModel(name="test", authors=["michel", "denis"], version="alpha")
-
basic_test(ext_md, MyExtension, validate=False)
--
GitLab
From 1f1feab1ea7c5960c267a692695af7dbe7d4c82e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 22:49:16 +0100
Subject: [PATCH 09/13] wip
---
stac_extension_genmeta/core.py | 6 +-
stac_extension_genmeta/schema.py | 121 +++++++++---------------------
stac_extension_genmeta/testing.py | 4 +-
tests/extensions_test.py | 8 +-
4 files changed, 49 insertions(+), 90 deletions(-)
diff --git a/stac_extension_genmeta/core.py b/stac_extension_genmeta/core.py
index ce5f35a..a83e350 100644
--- a/stac_extension_genmeta/core.py
+++ b/stac_extension_genmeta/core.py
@@ -43,6 +43,7 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
ExtensionManagementMixin[Union[pystac.Item, pystac.Collection]],
):
"""Custom extension class."""
+
def __init__(self, obj: T):
"""Initializer."""
if isinstance(obj, pystac.Item):
@@ -64,7 +65,7 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
self.md = model_cls(**props) if props else None
def __getattr__(self, item):
- """forward getattr to self.md."""
+ """Forward getattr to self.md."""
return getattr(self.md, item) if self.md else None
def apply(self, md: model_cls = None, **kwargs) -> None:
@@ -132,10 +133,12 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
class ItemCustomExtension(CustomExtension[pystac.Item]):
"""Item custom extension."""
+
pass
class AssetCustomExtension(CustomExtension[pystac.Asset]):
"""Asset custom extension."""
+
asset_href: str
properties: dict[str, Any]
additional_read_properties: Iterable[dict[str, Any]] | None = None
@@ -149,6 +152,7 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
class CollectionCustomExtension(CustomExtension[pystac.Collection]):
"""Collection curstom extension."""
+
properties: dict[str, Any]
def __init__(self, collection: pystac.Collection):
diff --git a/stac_extension_genmeta/schema.py b/stac_extension_genmeta/schema.py
index 53c6c57..35d33f6 100644
--- a/stac_extension_genmeta/schema.py
+++ b/stac_extension_genmeta/schema.py
@@ -1,11 +1,10 @@
+"""Generate the json schema."""
+
from pydantic import BaseModel
def generate_schema(
- model_cls: BaseModel,
- title: str,
- description: str,
- schema_uri: str
+ model_cls: BaseModel, title: str, description: str, schema_uri: str
) -> dict:
"""Generate the schema."""
properties = model_cls.model_json_schema()
@@ -22,116 +21,66 @@ def generate_schema(
"allOf": [
{
"type": "object",
- "required": [
- "type",
- "properties",
- "assets",
- "links"
- ],
+ "required": ["type", "properties", "assets", "links"],
"properties": {
- "type": {
- "const": "Feature"
- },
- "properties": {
- "$ref": "#/definitions/fields"
- },
- "assets": {
- "$ref": "#/definitions/assets"
- },
- "links": {
- "$ref": "#/definitions/links"
- }
- }
+ "type": {"const": "Feature"},
+ "properties": {"$ref": "#/definitions/fields"},
+ "assets": {"$ref": "#/definitions/assets"},
+ "links": {"$ref": "#/definitions/links"},
+ },
},
- {
- "$ref": "#/definitions/stac_extensions"
- }
- ]
+ {"$ref": "#/definitions/stac_extensions"},
+ ],
},
{
"$comment": "This is the schema for STAC Collections.",
"allOf": [
{
"type": "object",
- "required": [
- "type"
- ],
+ "required": ["type"],
"properties": {
- "type": {
- "const": "Collection"
- },
- "assets": {
- "$ref": "#/definitions/assets"
- },
- "item_assets": {
- "$ref": "#/definitions/assets"
- },
- "links": {
- "$ref": "#/definitions/links"
- }
- }
+ "type": {"const": "Collection"},
+ "assets": {"$ref": "#/definitions/assets"},
+ "item_assets": {"$ref": "#/definitions/assets"},
+ "links": {"$ref": "#/definitions/links"},
+ },
},
- {
- "$ref": "#/definitions/fields"
- },
- {
- "$ref": "#/definitions/stac_extensions"
- }
- ]
+ {"$ref": "#/definitions/fields"},
+ {"$ref": "#/definitions/stac_extensions"},
+ ],
},
{
"$comment": "This is the schema for STAC Catalogs.",
"allOf": [
{
"type": "object",
- "required": [
- "type"
- ],
+ "required": ["type"],
"properties": {
- "type": {
- "const": "Catalog"
- },
- "links": {
- "$ref": "#/definitions/links"
- }
- }
+ "type": {"const": "Catalog"},
+ "links": {"$ref": "#/definitions/links"},
+ },
},
- {
- "$ref": "#/definitions/fields"
- },
- {
- "$ref": "#/definitions/stac_extensions"
- }
- ]
- }
+ {"$ref": "#/definitions/fields"},
+ {"$ref": "#/definitions/stac_extensions"},
+ ],
+ },
],
"definitions": {
"stac_extensions": {
"type": "object",
- "required": [
- "stac_extensions"
- ],
+ "required": ["stac_extensions"],
"properties": {
"stac_extensions": {
"type": "array",
- "contains": {
- "const": schema_uri
- }
+ "contains": {"const": schema_uri},
}
- }
- },
- "links": {
- "type": "array",
- "items": {
- "$ref": "#/definitions/fields"
- }
+ },
},
+ "links": {"type": "array", "items": {"$ref": "#/definitions/fields"}},
"assets": {
"type": "object",
- "additionalProperties": {
- "$ref": "#/definitions/fields"
- }
+ "additionalProperties": {"$ref": "#/definitions/fields"},
},
- "fields": properties
- }
+ "fields": properties,
+ },
}
diff --git a/stac_extension_genmeta/testing.py b/stac_extension_genmeta/testing.py
index 40f8619..d6986e9 100644
--- a/stac_extension_genmeta/testing.py
+++ b/stac_extension_genmeta/testing.py
@@ -149,7 +149,9 @@ def is_schema_url_synced(cls):
local_schema = cls.get_schema()
url = cls.get_schema_uri()
url = (
- url.replace("/-/raw/main/", f"/-/raw/{CI_COMMIT_REF_NAME}/") if CI_COMMIT_REF_NAME else url
+ url.replace("/-/raw/main/", f"/-/raw/{CI_COMMIT_REF_NAME}/")
+ if CI_COMMIT_REF_NAME
+ else url
)
remote_schema = requests.get(url).json()
print(
diff --git a/tests/extensions_test.py b/tests/extensions_test.py
index 8e19920..69a332c 100644
--- a/tests/extensions_test.py
+++ b/tests/extensions_test.py
@@ -26,6 +26,10 @@ class MyExtensionMetadataModel(BaseExtensionModel):
def test_example():
"""Test example function."""
- MyExtension = create_extension_cls(model_cls=MyExtensionMetadataModel, schema_uri=SCHEMA_URI)
- ext_md = MyExtensionMetadataModel(name="test", authors=["michel", "denis"], version="alpha")
+ MyExtension = create_extension_cls(
+ model_cls=MyExtensionMetadataModel, schema_uri=SCHEMA_URI
+ )
+ ext_md = MyExtensionMetadataModel(
+ name="test", authors=["michel", "denis"], version="alpha"
+ )
basic_test(ext_md, MyExtension, validate=False)
--
GitLab
From 6feba1cd544164c065774252fc27b6d9594b34b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 22:53:15 +0100
Subject: [PATCH 10/13] wip
---
stac_extension_genmeta/core.py | 17 ++++-------------
stac_extension_genmeta/testing.py | 6 +++---
tests/extensions_test.py | 4 ++--
3 files changed, 9 insertions(+), 18 deletions(-)
diff --git a/stac_extension_genmeta/core.py b/stac_extension_genmeta/core.py
index a83e350..c46fff2 100644
--- a/stac_extension_genmeta/core.py
+++ b/stac_extension_genmeta/core.py
@@ -1,13 +1,13 @@
"""Generic metadata creation."""
+from collections.abc import Iterable
+import json
+import re
from typing import Any, Generic, TypeVar, Union, cast
from pystac.extensions.base import PropertiesExtension, ExtensionManagementMixin
import pystac
from pydantic import BaseModel, ConfigDict
-import re
-from collections.abc import Iterable
from .schema import generate_schema
-import json
class BaseExtensionModel(BaseModel):
@@ -17,16 +17,7 @@ class BaseExtensionModel(BaseModel):
def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExtension:
- """This method creates a pystac extension from a pydantic model.
-
- Args:
- model_cls: pydantic model class
- schema_uri: schema URI
-
- Returns:
- pystac extension class
-
- """
+ """This method creates a pystac extension from a pydantic model."""
# check URI
if not re.findall(r"(?:(\/v\d\.(?:\d+\.)*\d+\/+))", schema_uri):
diff --git a/stac_extension_genmeta/testing.py b/stac_extension_genmeta/testing.py
index d6986e9..23c5bc8 100644
--- a/stac_extension_genmeta/testing.py
+++ b/stac_extension_genmeta/testing.py
@@ -1,12 +1,12 @@
"""Testing module."""
import os
-import pystac
-from datetime import datetime
import random
import json
-import requests
import difflib
+from datetime import datetime
+import requests
+import pystac
def create_dummy_item(date=None):
diff --git a/tests/extensions_test.py b/tests/extensions_test.py
index 69a332c..6fcf78c 100644
--- a/tests/extensions_test.py
+++ b/tests/extensions_test.py
@@ -1,9 +1,9 @@
"""Tests example."""
-from stac_extension_genmeta import create_extension_cls, BaseExtensionModel
-from stac_extension_genmeta.testing import basic_test
from pydantic import Field
from typing import List, Final
+from stac_extension_genmeta import create_extension_cls, BaseExtensionModel
+from stac_extension_genmeta.testing import basic_test
# Extension parameters
SCHEMA_URI: Final = "https://example.com/image-process/v1.0.0/schema.json"
--
GitLab
From 9d4812f54d4575fe3e650f3b752321f2fd294590 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 23:07:54 +0100
Subject: [PATCH 11/13] wip
---
stac_extension_genmeta/core.py | 8 +++-----
stac_extension_genmeta/testing.py | 10 ++++------
tests/extensions_test.py | 5 +++--
3 files changed, 10 insertions(+), 13 deletions(-)
diff --git a/stac_extension_genmeta/core.py b/stac_extension_genmeta/core.py
index c46fff2..10dcf76 100644
--- a/stac_extension_genmeta/core.py
+++ b/stac_extension_genmeta/core.py
@@ -103,7 +103,7 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
@classmethod
def export_schema(cls, json_file):
"""Export schema."""
- with open(json_file, "w") as f:
+ with open(json_file, "w", encoding="utf-8") as f:
json.dump(cls.get_schema(), f, indent=2)
@classmethod
@@ -112,10 +112,10 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
if isinstance(obj, pystac.Item):
cls.ensure_has_extension(obj, add_if_missing)
return cast(CustomExtension[T], ItemCustomExtension(obj))
- elif isinstance(obj, pystac.Asset):
+ if isinstance(obj, pystac.Asset):
cls.ensure_owner_has_extension(obj, add_if_missing)
return cast(CustomExtension[T], AssetCustomExtension(obj))
- elif isinstance(obj, pystac.Collection):
+ if isinstance(obj, pystac.Collection):
cls.ensure_has_extension(obj, add_if_missing)
return cast(CustomExtension[T], CollectionCustomExtension(obj))
raise pystac.ExtensionTypeError(
@@ -125,8 +125,6 @@ def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExt
class ItemCustomExtension(CustomExtension[pystac.Item]):
"""Item custom extension."""
- pass
-
class AssetCustomExtension(CustomExtension[pystac.Asset]):
"""Asset custom extension."""
diff --git a/stac_extension_genmeta/testing.py b/stac_extension_genmeta/testing.py
index 23c5bc8..319ae16 100644
--- a/stac_extension_genmeta/testing.py
+++ b/stac_extension_genmeta/testing.py
@@ -63,7 +63,6 @@ METHODS = ["arg", "md", "dict"]
def basic_test(
ext_md,
ext_cls,
- item_test: bool = True,
asset_test: bool = True,
collection_test: bool = True,
validate: bool = True,
@@ -120,7 +119,7 @@ def basic_test(
def test_collection(method):
"""Test extension against collection."""
- item, col = create_dummy_item()
+ _, col = create_dummy_item()
print_item(col)
apply(col, method)
print_item(col)
@@ -130,9 +129,8 @@ def basic_test(
comp(col)
for method in METHODS:
- if item_test:
- print(f"Test item with {method} args passing strategy")
- test_item(method)
+ print(f"Test item with {method} args passing strategy")
+ test_item(method)
if asset_test:
print(f"Test asset with {method} args passing strategy")
test_asset(method)
@@ -153,7 +151,7 @@ def is_schema_url_synced(cls):
if CI_COMMIT_REF_NAME
else url
)
- remote_schema = requests.get(url).json()
+ remote_schema = requests.get(url, timeout=10).json()
print(
f"Local schema is :\n"
f"{local_schema}\n"
diff --git a/tests/extensions_test.py b/tests/extensions_test.py
index 6fcf78c..bbae3cb 100644
--- a/tests/extensions_test.py
+++ b/tests/extensions_test.py
@@ -1,7 +1,7 @@
"""Tests example."""
-from pydantic import Field
from typing import List, Final
+from pydantic import Field
from stac_extension_genmeta import create_extension_cls, BaseExtensionModel
from stac_extension_genmeta.testing import basic_test
@@ -11,6 +11,7 @@ PREFIX: Final = "some_prefix:"
NAME: Final = PREFIX + "name"
AUTHORS: Final = PREFIX + "authors"
VERSION: Final = PREFIX + "version"
+OPT_FIELD: Final = PREFIX + "opt_field"
class MyExtensionMetadataModel(BaseExtensionModel):
@@ -20,7 +21,7 @@ class MyExtensionMetadataModel(BaseExtensionModel):
authors: List[str] = Field(title="Authors", alias=AUTHORS)
version: str = Field(title="Process version", alias=VERSION)
opt_field: str | None = Field(
- title="Some optional field", alias=f"{PREFIX}:opt_field", default=None
+ title="Some optional field", alias=OPT_FIELD, default=None
)
--
GitLab
From 981506e1336e51b9361fdda8ccc8d9b23c1e2388 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 23:21:58 +0100
Subject: [PATCH 12/13] wip
---
README.md | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/README.md b/README.md
index 71f0b57..017b99c 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,13 @@
This module is a helper to build STAC extensions carrying metadata defined with
pydantic models.
+## Installation
+
+```
+PIP_EXTRA_INDEX_URL=https://forgemia.inra.fr/api/v4/projects/10919/packages/pypi/simple
+pip install stac-extension-genmeta
+```
+
## Example
Simple example in 4 steps.
--
GitLab
From bb1dd68d7e17687224f018141aad5a3e2dab2af5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi?= <remi.cresson@inrae.fr>
Date: Thu, 13 Feb 2025 23:24:40 +0100
Subject: [PATCH 13/13] wip
---
stac_extension_genmeta/core.py | 2 --
1 file changed, 2 deletions(-)
diff --git a/stac_extension_genmeta/core.py b/stac_extension_genmeta/core.py
index 10dcf76..2f53023 100644
--- a/stac_extension_genmeta/core.py
+++ b/stac_extension_genmeta/core.py
@@ -18,8 +18,6 @@ class BaseExtensionModel(BaseModel):
def create_extension_cls(model_cls: BaseModel, schema_uri: str) -> PropertiesExtension:
"""This method creates a pystac extension from a pydantic model."""
-
- # check URI
if not re.findall(r"(?:(\/v\d\.(?:\d+\.)*\d+\/+))", schema_uri):
raise ValueError(
"The schema_uri must contain the version in the form 'vX.Y.Z'"
--
GitLab