deep-code 0.0.1.dev0__py3-none-any.whl

deep_code/utils/osc_extension.py

@@ -0,0 +1,201 @@
+#!/usr/bin/env python3
+
+# Copyright (c) 2025 by Brockmann Consult GmbH
+# Permissions are hereby granted under the terms of the MIT License:
+# https://opensource.org/licenses/MIT.
+
+from typing import Literal
+
+import pystac
+from pystac import Extent, SpatialExtent, TemporalExtent
+from pystac.extensions.base import ExtensionManagementMixin, PropertiesExtension
+
+from deep_code.constants import CF_SCHEMA_URI, OSC_SCHEMA_URI
+
+
+class OscExtension(
+    PropertiesExtension, ExtensionManagementMixin[pystac.Item | pystac.Collection]
+):
+    """Handles the OSC extension for STAC Items and Collections.
+
+    Args:
+        obj: The STAC Item or Collection to which the OSC extension is applied.
+    """
+
+    name: Literal["osc"] = "osc"
+
+    def __init__(self, obj: pystac.Item | pystac.Collection):
+        if isinstance(obj, pystac.Collection):
+            self.properties = obj.extra_fields
+        else:
+            self.properties = obj.properties
+        self.obj = obj
+
+    @property
+    def osc_type(self) -> str | None:
+        return self._get_property("osc:type", str)
+
+    @osc_type.setter
+    def osc_type(self, v: str) -> None:
+        self._set_property("osc:type", v, pop_if_none=False)
+
+    @property
+    def osc_name(self) -> str | None:
+        return self._get_property("osc:name", str)
+
+    @osc_name.setter
+    def osc_name(self, v: str) -> None:
+        self._set_property("osc:name", v, pop_if_none=False)
+
+    @property
+    def osc_status(self) -> str | None:
+        return self._get_property("osc:status", str)
+
+    @osc_status.setter
+    def osc_status(self, value: str) -> None:
+        self._set_property("osc:status", value, pop_if_none=False)
+
+    @property
+    def osc_project(self) -> str | None:
+        return self._get_property("osc:project", str)
+
+    @osc_project.setter
+    def osc_project(self, v: str) -> None:
+        self._set_property("osc:project", v, pop_if_none=False)
+
+    @property
+    def osc_themes(self) -> list[str] | None:
+        return self._get_property("osc:themes", list)
+
+    @osc_themes.setter
+    def osc_themes(self, value: list[str]) -> None:
+        if not isinstance(value, list) or not all(
+            isinstance(item, str) for item in value
+        ):
+            raise ValueError("osc:themes must be a list of strings")
+        self._set_property("osc:themes", value, pop_if_none=False)
+
+    @property
+    def osc_region(self) -> str | None:
+        return self._get_property("osc:region", str)
+
+    @osc_region.setter
+    def osc_region(self, value: str) -> None:
+        self._set_property("osc:region", value, pop_if_none=False)
+
+    @property
+    def osc_missions(self) -> list[str] | None:
+        return self._get_property("osc:missions", list)
+
+    @osc_missions.setter
+    def osc_missions(self, value: list[str]) -> None:
+        if not isinstance(value, list) or not all(
+            isinstance(item, str) for item in value
+        ):
+            raise ValueError("osc:missions must be a list of strings")
+        self._set_property("osc:missions", value, pop_if_none=False)
+
+    def set_extent(self, spatial: list[list[float]], temporal: list[list[str]]) -> None:
+        self.obj.extent = Extent(SpatialExtent(spatial), TemporalExtent(temporal))
+
+    @property
+    def osc_variables(self) -> list[str] | None:
+        return self._get_property("osc:variables", list)
+
+    @osc_variables.setter
+    def osc_variables(self, v: list[str]) -> None:
+        if not isinstance(v, list) or not all(isinstance(item, str) for item in v):
+            raise ValueError("osc:variables must be a list of strings")
+        self._set_property("osc:variables", v, pop_if_none=False)
+
+    @property
+    def keywords(self) -> list[str] | None:
+        return self._get_property("keywords", list)
+
+    @keywords.setter
+    def keywords(self, value: list[str]) -> None:
+        if not isinstance(value, list) or not all(
+            isinstance(item, str) for item in value
+        ):
+            raise ValueError("keywords must be a list of strings")
+        self._set_property("keywords", value, pop_if_none=False)
+
+    @property
+    def cf_parameter(self) -> list[dict] | None:
+        return self._get_property("cf:parameter", list)
+
+    @cf_parameter.setter
+    def cf_parameter(self, value: list[dict]) -> None:
+        if not isinstance(value, list) or not all(
+            isinstance(item, dict) for item in value
+        ):
+            raise ValueError("cf:parameter must be a list of dictionaries")
+        self._set_property("cf:parameter", value, pop_if_none=False)
+
+    @property
+    def created(self) -> str | None:
+        return self._get_property("created", str)
+
+    @created.setter
+    def created(self, value: str) -> None:
+        self._set_property("created", value, pop_if_none=False)
+
+    @property
+    def updated(self) -> str | None:
+        return self._get_property("updated", str)
+
+    @updated.setter
+    def updated(self, value: str) -> None:
+        self._set_property("updated", value, pop_if_none=False)
+
+    @classmethod
+    def get_schema_uri(cls) -> list[str]:
+        return [OSC_SCHEMA_URI, CF_SCHEMA_URI]
+
+    @classmethod
+    def ext(
+        cls, obj: pystac.Item | pystac.Collection, add_if_missing: bool = False
+    ) -> "OscExtension":
+        """Returns the OscExtension instance for the given object, adding the extension
+        if missing."""
+        if cls.has_extension(obj):
+            return OscExtension(obj)
+        elif add_if_missing:
+            return cls.add_to(obj)
+        else:
+            raise ValueError(
+                "OSC extension is not present and add_if_missing is False."
+            )
+
+    @classmethod
+    def has_extension(cls, obj: pystac.Item | pystac.Collection) -> bool:
+        """Checks if all required extensions are present."""
+        schema_uris = cls.get_schema_uri()
+        if isinstance(schema_uris, list):
+            return all(uri in obj.stac_extensions for uri in schema_uris)
+        elif isinstance(schema_uris, str):
+            return schema_uris in obj.stac_extensions
+
+    @classmethod
+    def add_to(cls, obj: pystac.Item | pystac.Collection) -> "OscExtension":
+        """Adds the OSC and CF extensions to the object's extensions."""
+        schema_uris = cls.get_schema_uri()
+        if isinstance(schema_uris, list):  # Handle list of URIs
+            for uri in schema_uris:
+                if uri not in obj.stac_extensions:
+                    obj.stac_extensions.append(uri)
+        elif isinstance(schema_uris, str):  # Handle single URI
+            if schema_uris not in obj.stac_extensions:
+                obj.stac_extensions.append(schema_uris)
+        return OscExtension(obj)
+
+    def validate_extension(self) -> None:
+        """Validates that all required fields for the OSC extension are set."""
+        required_fields = ["osc:type", "osc:project", "osc:status"]
+        missing_fields = [
+            field
+            for field in required_fields
+            if self._get_property(field, None) is None
+        ]
+        if missing_fields:
+            raise ValueError(f"Missing required fields: {', '.join(missing_fields)}")

deep_code/version.py

@@ -0,0 +1,22 @@
+# The MIT License (MIT)
+# Copyright (c) 2024 by DeepESDL and Brockmann Consult GmbH
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NON INFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+version = "0.0.1.dev0"

deep_code-0.0.1.dev0.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 DeepESDL and Brockmann Consult GmbH
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

deep_code-0.0.1.dev0.dist-info/METADATA

@@ -0,0 +1,166 @@
+Metadata-Version: 2.2
+Name: deep_code
+Version: 0.0.1.dev0
+Summary: deepesdl earthcode integration utility tool
+Author-email: Tejas Morbagal Harish <tejas.morbagalharish@brockmann-consult.de>
+License: MIT
+Project-URL: Repository, https://github.com/deepesdl/deep-code
+Project-URL: Issues, https://github.com/deepesdl/deep-code/issues
+Project-URL: Changelog, https://github.com/deepesdl/deep-code/blob/main/CHANGES.md
+Keywords: analysis ready data,data science,datacube,xarray,zarr,xcube,stac,FAIR,reproducible workflow,DeepESDL
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: fsspec
+Requires-Dist: jsonschema
+Requires-Dist: requests
+Requires-Dist: pandas
+Requires-Dist: pystac
+Requires-Dist: pyyaml
+Requires-Dist: xcube-core
+Requires-Dist: xrlint
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: numpy; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-recording; extra == "dev"
+
+# deep-code
+
+[![Build Status](https://github.com/deepesdl/deep-code/actions/workflows/unittest-workflow.yaml/badge.svg)](https://github.com/deepesdl/deep-code/actions/workflows/unittest-workflow.yaml)
+[![codecov](https://codecov.io/gh/deepesdl/deep-code/graph/badge.svg?token=47MQXOXWOK)](https://codecov.io/gh/deepesdl/deep-code)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![License](https://img.shields.io/github/license/dcs4cop/xcube-smos)](https://github.com/deepesdl/deep-code/blob/main/LICENSE)
+
+`deep-code` is a lightweight python tool that comprises a command line interface(CLI) 
+and Python API providing utilities that aid integration of DeepESDL datasets, 
+experiments with EarthCODE.
+
+The first release will focus on implementing the publish feature of DeepESDL 
+experiments/workflow as OGC API record and Datasets as an OSC stac collection.
+
+## Setup
+
+## Install
+`deep-code` will be available in PyPI and conda-forge. Till the stable release,
+developers/contributors can follow the below steps to install deep-code.
+
+## Installing from the repository for Developers/Contributors
+
+To install deep-code directly from the git repository, clone the repository, and execute the steps below:
+
+```commandline
+conda env create
+conda activate deep-code
+pip install -e .
+```
+
+This installs all the dependencies of `deep-code` into a fresh conda environment, 
+and installs deep-code from the repository into the same environment.
+
+## Testing
+
+To run the unit test suite:
+
+```commandline
+pytest
+```
+
+To analyze test coverage
+```shell
+pytest --cov=deep-code
+```
+
+To produce an HTML coverage report
+
+```commandline
+pytest --cov-report html --cov=deep-code
+```
+
+## deep_code usage
+
+`deep_code` provides a command-line tool called deep-code, which has several subcommands 
+providing different utility functions.
+Use the --help option with these subcommands to get more details on usage.
+
+###  deep-code publish-product
+
+Publish a dataset which is a result of an experiment to the EarthCODE 
+open-science catalog.
+
+```commandline
+ deep-code publish-dataset /path/to/dataset-config.yaml
+ ```
+
+#### .gitaccess example
+
+```
+github-username: your-git-user
+github-token: personal access token
+```
+
+#### dataset-config.yaml example
+
+```
+dataset_id: hydrology-1D-0.009deg-100x60x60-3.0.2.zarr
+collection_id: hydrology
+osc_themes:
+  - Land
+  - Oceans
+# non-mandatory
+documentation_link: https://deepesdl.readthedocs.io/en/latest/datasets/hydrology-1D-0.009deg-100x60x60-3.0.2.zarr/
+access_link: s3://test
+dataset_status: completed
+osc_region: global
+cf_parameter:
+  - name: hydrology
+```
+
+dataset-id has to be a valid dataset-id from `deep-esdl-public` s3 or your team bucket.
+
+### deep-code publish-workflow
+
+Publish a workflow/experiment to the EarthCODE open-science catalog.
+
+```commandline
+deep-code publish-workflow /path/to/workflow-config.yaml
+ ```
+#### workflow-config.yaml example
+
+```
+workflow_id: "4D Med hydrology cube generation"
+properties:
+  title: "Hydrology cube generation recipe"
+  description: "4D Med cube generation"
+  keywords:
+    - Earth Science
+  themes:
+      - Atmosphere
+      - Ocean
+      - Evaporation
+  license: proprietary
+  jupyter_kernel_info:
+    name: deepesdl-xcube-1.7.1
+    python_version: 3.11
+    env_file: https://git/env.yml
+links:
+  - rel: "documentation"
+    type: "application/json"
+    title: "4DMed Hydrology Cube Generation Recipe"
+    href: "https://github.com/deepesdl/cube-gen/tree/main/hydrology/README.md"
+  - rel: "jupyter-notebook"
+    type: "application/json"
+    title: "Workflow Jupyter Notebook"
+    href: "https://github.com/deepesdl/cube-gen/blob/main/hydrology/notebooks/reading_hydrology.ipynb"
+contact:
+  - name: Tejas Morbagal Harish
+    organization: Brockmann Consult GmbH
+    links:
+      - rel: "about"
+        type: "text/html"
+        href: "https://www.brockmann-consult.de/"
+```

deep_code-0.0.1.dev0.dist-info/RECORD

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+deep_code-0.0.1.dev0.dist-info/LICENSE,sha256=bzOmAfwEn0ijhaLp6cZEjv227VjpKNq-tkQoCqcEX68,1092
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deep_code-0.0.1.dev0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (75.8.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

deep_code-0.0.1.dev0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+deep-code = deep_code.cli.main:main

deep_code-0.0.1.dev0.dist-info/top_level.txt

@@ -0,0 +1 @@
+deep_code