Merge pull request #37 from pepkit/dev

Release 0.4.0

.github/workflows/pytest-windows.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         os: [windows-latest]
 
     steps:

.github/workflows/pytest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         os: [ubuntu-20.04]
 
     steps:

MANIFEST.in

@@ -1,3 +1,4 @@
 include requirements/*
 include README.md
-include pephubclient/pephub_oauth/*
+include pephubclient/pephub_oauth/*
+include pephubclient/modules/*

Makefile

@@ -5,7 +5,7 @@ run-coverage:
 	coverage run -m pytest
 
 html-report:
-	coverage html
+	coverage html --omit="*/test*"
 
 open-coverage:
 	cd htmlcov && google-chrome index.html

docs/changelog.md

@@ -2,8 +2,26 @@
 
 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.
 
+## [0.4.0] - 2024-02-12
+### Added
+- a parameter that points to where peps should be saved ([#32](https://github.com/pepkit/pephubclient/issues/32))
+- pep zipping option to `save_pep` function ([#34](https://github.com/pepkit/pephubclient/issues/34))
+- API for samples ([#29](https://github.com/pepkit/pephubclient/issues/29))
+- API for projects ([#28](https://github.com/pepkit/pephubclient/issues/28))
+
+### Updated
+- Transferred `save_pep` function to helpers
+
 ## [0.3.0] - 2024-01-17
 ### Added
+- customization of the base PEPhub URL ([#22](https://github.com/pepkit/pephubclient/issues/22))
+
+### Updated
+- Updated PEPhub API URL
+- Increased the required pydantic version to >2.5.0
+
+## [0.2.2] - 2024-01-17
+### Added
 - customization of the base pephub URL. [#22](https://github.com/pepkit/pephubclient/issues/22)
 
 ### Updated 

pephubclient/__init__.py

@@ -1,8 +1,26 @@
 from pephubclient.pephubclient import PEPHubClient
+from pephubclient.helpers import is_registry_path, save_pep
+import logging
+import coloredlogs
 
 __app_name__ = "pephubclient"
-__version__ = "0.2.2"
+__version__ = "0.4.0"
 __author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
 
 
-__all__ = ["PEPHubClient", __app_name__, __author__, __version__]
+__all__ = [
+    "PEPHubClient",
+    __app_name__,
+    __author__,
+    __version__,
+    "is_registry_path",
+    "save_pep",
+]
+
+
+_LOGGER = logging.getLogger(__app_name__)
+coloredlogs.install(
+    logger=_LOGGER,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] %(message)s",
+)

pephubclient/cli.py

@@ -29,6 +29,8 @@ def logout():
 def pull(
     project_registry_path: str,
     force: bool = typer.Option(False, help="Overwrite project if it exists."),
+    zip: bool = typer.Option(False, help="Save project as zip file."),
+    output: str = typer.Option(None, help="Output directory."),
 ):
     """
     Download and save project locally.
@@ -37,6 +39,8 @@ def pull(
         _client.pull,
         project_registry_path=project_registry_path,
         force=force,
+        output=output,
+        zip=zip,
     )
 
 

pephubclient/constants.py

@@ -12,12 +12,18 @@
 PEPHUB_PEP_SEARCH_URL = f"{PEPHUB_BASE_URL}api/v1/namespaces/{{namespace}}/projects"
 PEPHUB_PUSH_URL = f"{PEPHUB_BASE_URL}api/v1/namespaces/{{namespace}}/projects/json"
 
+PEPHUB_SAMPLE_URL = f"{PEPHUB_BASE_URL}api/v1/projects/{{namespace}}/{{project}}/samples/{{sample_name}}"
+PEPHUB_VIEW_URL = (
+    f"{PEPHUB_BASE_URL}api/v1/projects/{{namespace}}/{{project}}/views/{{view_name}}"
+)
+PEPHUB_VIEW_SAMPLE_URL = f"{PEPHUB_BASE_URL}api/v1/projects/{{namespace}}/{{project}}/views/{{view_name}}/{{sample_name}}"
+
 
 class RegistryPath(BaseModel):
-    protocol: Optional[str]
+    protocol: Optional[str] = None
     namespace: str
     item: str
-    subitem: Optional[str]
+    subitem: Optional[str] = None
     tag: Optional[str] = "default"
 
     @field_validator("tag")
@@ -33,3 +39,10 @@ class ResponseStatusCodes(int, Enum):
     NOT_EXIST = 404
     CONFLICT = 409
     INTERNAL_ERROR = 500
+
+
+USER_DATA_FILE_NAME = "jwt.txt"
+HOME_PATH = os.getenv("HOME")
+if not HOME_PATH:
+    HOME_PATH = os.path.expanduser("~")
+PATH_TO_FILE_WITH_JWT = os.path.join(HOME_PATH, ".pephubclient/") + USER_DATA_FILE_NAME

pephubclient/files_manager.py

@@ -4,8 +4,8 @@
 
 import pandas
 import yaml
+import zipfile
 
-from pephubclient.constants import RegistryPath
 from pephubclient.exceptions import PEPExistsError
 
 
@@ -29,17 +29,23 @@ def load_jwt_data_from_file(path: str) -> str:
                 return f.read()
 
     @staticmethod
-    def create_project_folder(registry_path: RegistryPath) -> str:
+    def create_project_folder(
+        parent_path: str,
+        folder_name: str,
+    ) -> str:
         """
         Create new project folder
 
-        :param registry_path: project registry path
+        :param parent_path: parent path to create folder in
+        :param folder_name: folder name
         :return: folder_path
         """
-        folder_name = FilesManager._create_filename_to_save_downloaded_project(
-            registry_path
-        )
-        folder_path = os.path.join(os.getcwd(), folder_name)
+        if parent_path:
+            if not Path(parent_path).exists():
+                raise OSError(
+                    f"Parent path does not exist. Provided path: {parent_path}"
+                )
+        folder_path = os.path.join(parent_path or os.getcwd(), folder_name)
         Path(folder_path).mkdir(parents=True, exist_ok=True)
         return folder_path
 
@@ -62,21 +68,28 @@ def file_exists(full_path: str) -> bool:
     def delete_file_if_exists(filename: str) -> None:
         with suppress(FileNotFoundError):
             os.remove(filename)
-
-    @staticmethod
-    def _create_filename_to_save_downloaded_project(registry_path: RegistryPath) -> str:
-        """
-        Takes query string and creates output filename to save the project to.
-
-        :param registry_path: Query string that was used to find the project.
-        :return: Filename uniquely identifying the project.
-        """
-        filename = "_".join(filter(bool, [registry_path.namespace, registry_path.item]))
-        if registry_path.tag:
-            filename += f":{registry_path.tag}"
-        return filename
+            print(
+                f"\033[38;5;11m{f'File was deleted successfully -> {filename}'}\033[0m"
+            )
 
     @staticmethod
     def check_writable(path: str, force: bool = True):
         if not force and os.path.isfile(path):
             raise PEPExistsError(f"File already exists and won't be updated: {path}")
+
+    @staticmethod
+    def save_zip_file(files_dict: dict, file_path: str, force: bool = False) -> None:
+        """
+        Save zip file with provided files as dict.
+
+        :param files_dict: dict with files to save. e.g. {"file1.txt": "file1 content"}
+        :param file_path: filename to save zip file to
+        :param force: overwrite file if exists
+        :return: None
+        """
+        FilesManager.check_writable(path=file_path, force=force)
+        with zipfile.ZipFile(
+            file_path, mode="w", compression=zipfile.ZIP_DEFLATED
+        ) as zf:
+            for name, res in files_dict.items():
+                zf.writestr(name, str.encode(res))