Rlease v0.5.0

.github/workflows/black_linter.yml

@@ -8,6 +8,6 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - uses: psf/black@stable

.github/workflows/pytest-windows.yml

@@ -15,10 +15,10 @@ jobs:
         os: [windows-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/pytest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.12"]
+        python-version: ["3.9", "3.13"]
         os: [ubuntu-20.04]
 
     steps:

.github/workflows/python-publish.yml

@@ -11,9 +11,9 @@ jobs:
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

MANIFEST.in

@@ -1,4 +1,5 @@
 include requirements/*
 include README.md
 include pephubclient/pephub_oauth/*
-include pephubclient/modules/*
+include pephubclient/modules/*
+include pephubclient/schemas/*

Taskfile.yaml

@@ -0,0 +1,7 @@
+version: '3'
+
+tasks:
+  hello:
+    cmds:
+      - black .
+    silent: false

docs/changelog.md

@@ -1,8 +1,12 @@
 # Changelog
-
+  
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
 
+## [0.5.0] - 2025-03-31
+### Added
+- Added schemas CLI and Python methods for fetching schemas from PEPhub
+
 ## [0.4.5] - 2024-11-21
 ### Added
 - Function for unwrapping PEPhub registry path

pephubclient/__init__.py

@@ -4,7 +4,7 @@
 import coloredlogs
 
 __app_name__ = "pephubclient"
-__version__ = "0.4.5"
+__version__ = "0.5.0"
 __author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
 
 

pephubclient/cli.py

@@ -3,6 +3,7 @@
 from pephubclient import __app_name__, __version__
 from pephubclient.helpers import call_client_func
 from pephubclient.pephubclient import PEPHubClient
+from pephubclient.schemas.schema_cli import schemas_app
 
 _client = PEPHubClient()
 
@@ -88,3 +89,6 @@ def common(
     ),
 ):
     pass
+
+
+app.add_typer(schemas_app, name="schema")

pephubclient/exceptions.py

@@ -31,3 +31,11 @@ class PEPExistsError(BasePephubclientException):
     def __init__(self, message: Optional[str] = None):
         self.message = message
         super().__init__(self.message or self.default_message)
+
+
+class FileDoesNotExistError(BasePephubclientException):
+    default_message = "File does not exist."
+
+    def __init__(self, message: Optional[str] = None):
+        self.message = message
+        super().__init__(self.message or self.default_message)

pephubclient/helpers.py

@@ -1,7 +1,8 @@
 import json
-from typing import Any, Callable, Optional, Union
+from typing import Any, Callable, Optional, Union, Literal, Tuple
 import peppy
 import yaml
+from pathlib import Path
 import os
 import pandas as pd
 from peppy.const import (
@@ -21,7 +22,11 @@
 from ubiquerg import parse_registry_path
 from pydantic import ValidationError
 
-from pephubclient.exceptions import PEPExistsError, ResponseError
+from pephubclient.exceptions import (
+    PEPExistsError,
+    ResponseError,
+    BasePephubclientException,
+)
 from pephubclient.constants import RegistryPath
 from pephubclient.files_manager import FilesManager
 from pephubclient.models import ProjectDict
@@ -322,3 +327,80 @@ def save_pep(
         parent_path=project_path, folder_name=file_name
     )
     _save_unzipped_pep(project, folder_path, force=force)
+
+
+def open_schema(file_path: Union[str, Path]) -> dict:
+    """
+    Open schema file that are saved in yaml or json format.
+
+    :param file_path: path to the schema file
+
+    :raises: FileNotFoundError - if file doesn't exist
+    :return: file object in dict format
+    """
+    if isinstance(file_path, str):
+        file_path = Path(file_path)
+
+    if not file_path.is_file():
+        raise FileNotFoundError(
+            f"Provided schema file doesn't exist. File path: `{str(file_path)}`"
+        )
+
+    if file_path.suffix == ".yaml" or file_path.suffix == ".yml":
+        with open(file_path, "r") as file:
+            data = yaml.safe_load(file)
+
+    elif file_path.suffix == ".json":
+        with open(file_path, "r") as file:
+            data = json.load(file)
+    else:
+        raise BasePephubclientException(
+            f"Incorrect file format provided: '{file_path.suffix}'. "
+            "Only yaml and json formats are supported."
+        )
+
+    return data
+
+
+def save_schema(
+    file_path: Union[str, Path],
+    schema_obj: dict,
+    format: Literal["json", "yaml"] = "yaml",
+) -> None:
+    """
+    Save dict object as file in json or yaml format
+
+    :param file_path: path to the file
+    :param schema_obj: content to be saved in the file
+    :param format: Format in which file should be saved on disc. Default: yaml
+
+    :return: File path.
+    """
+
+    if format == "yaml":
+        schema_obj = yaml.dump(schema_obj)
+
+    elif format == "json":
+        schema_obj = json.dumps(schema_obj, indent=4)
+    else:
+        raise BasePephubclientException(f"Incorrect format provided: '{format}'")
+
+    with open(file_path, "w") as file:
+        file.write(schema_obj)
+
+
+def schema_path_converter(schema_path: str) -> Tuple[str, str, str]:
+    """
+    Convert schema path to namespace, name
+
+    :param schema_path: schema path that has structure: "namespace/name.yaml"
+    :return: tuple(namespace, name, version)
+    """
+    if "/" in schema_path:
+        namespace, name_tag = schema_path.split("/")
+        if ":" in name_tag:
+            name, version = name_tag.split(":")
+            return namespace, name, version
+
+        return namespace, name_tag, "latest"
+    raise BasePephubclientException(f"Error in: '{schema_path}'")

pephubclient/pephubclient.py

@@ -30,6 +30,7 @@
 from pephubclient.pephub_oauth.pephub_oauth import PEPHubAuth
 from pephubclient.modules.view import PEPHubView
 from pephubclient.modules.sample import PEPHubSample
+from pephubclient.schemas.schema import PEPHubSchema
 
 urllib3.disable_warnings()
 
@@ -40,6 +41,7 @@ def __init__(self):
 
         self.__view = PEPHubView(self.__jwt_data)
         self.__sample = PEPHubSample(self.__jwt_data)
+        self.__schema = PEPHubSchema(self.__jwt_data)
 
     @property
     def view(self) -> PEPHubView:
@@ -49,6 +51,10 @@ def view(self) -> PEPHubView:
     def sample(self) -> PEPHubSample:
         return self.__sample
 
+    @property
+    def schema(self) -> PEPHubSchema:
+        return self.__schema
+
     def login(self) -> NoReturn:
         """
         Log in to PEPhub

pephubclient/schemas/constants.py

@@ -0,0 +1,17 @@
+from pephubclient.constants import PEPHUB_BASE_URL
+
+PEPHUB_SCHEMA_BASE_URL = f"{PEPHUB_BASE_URL}api/v1/schemas/"
+
+PEPHUB_SCHEMA_NEW_SCHEMA_URL = f"{PEPHUB_SCHEMA_BASE_URL}{{namespace}}/json"
+PEPHUB_SCHEMA_NEW_VERSION_URL = (
+    f"{PEPHUB_SCHEMA_BASE_URL}{{namespace}}/{{schema_name}}/versions/json"
+)
+PEPHUB_SCHEMA_RECORD_URL = f"{PEPHUB_SCHEMA_BASE_URL}{{namespace}}/{{schema_name}}"
+PEPHUB_SCHEMA_VERSIONS_URL = (
+    f"{PEPHUB_SCHEMA_BASE_URL}{{namespace}}/{{schema_name}}/versions"
+)
+PEPHUB_SCHEMA_VERSION_URL = (
+    f"{PEPHUB_SCHEMA_BASE_URL}{{namespace}}/{{schema_name}}/versions/{{version}}"
+)
+
+LATEST_VERSION = "latest"

pephubclient/schemas/models.py

@@ -0,0 +1,77 @@
+from pydantic import BaseModel, ConfigDict
+from typing import Optional, Dict, Union, List
+import datetime
+
+
+class PaginationResult(BaseModel):
+    page: int = 0
+    page_size: int = 10
+    total: int
+
+
+class SchemaVersionAnnotation(BaseModel):
+    """
+    Schema version annotation model
+    """
+
+    namespace: str
+    schema_name: str
+    version: str
+    contributors: Optional[str] = ""
+    release_notes: Optional[str] = ""
+    tags: Dict[str, Union[str, None]] = {}
+    release_date: datetime.datetime
+    last_update_date: datetime.datetime
+
+
+class SchemaVersionResult(BaseModel):
+    pagination: PaginationResult
+    results: List[SchemaVersionAnnotation]
+
+
+class NewSchemaVersionModel(BaseModel):
+    """
+    Model for creating a new schema version from json
+    """
+
+    contributors: Union[str, None] = None
+    release_notes: Union[str, None] = None
+    tags: Optional[Union[List[str], str, Dict[str, str], List[Dict[str, str]]]] = (
+        None,
+    )
+    version: str
+    schema_value: dict
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class NewSchemaRecordModel(NewSchemaVersionModel):
+    """
+    Model for creating a new schema record from json
+    """
+
+    schema_name: str
+    description: Union[str, None] = None
+    maintainers: Union[str, None] = None
+    lifecycle_stage: Union[str, None] = None
+    private: bool = False
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class UpdateSchemaRecordFields(BaseModel):
+    maintainers: Optional[Union[str, None]] = None
+    lifecycle_stage: Optional[Union[str, None]] = None
+    private: Optional[bool] = None
+    name: Optional[Union[str, None]] = None
+    description: Optional[Union[str, None]] = None
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class UpdateSchemaVersionFields(BaseModel):
+    contributors: Optional[Union[str, None]] = None
+    schema_value: Optional[Union[str, None]] = None
+    release_notes: Optional[Union[str, None]] = None
+
+    model_config = ConfigDict(extra="forbid")