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Merge pull request #21 from pepkit/dev
Release v0.1.1
2 parents 75f2303 + 59249fb commit b7185dd

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‎.github/workflows/pytest.yml

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@@ -32,4 +32,4 @@ jobs:
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run: python -m pip install .
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- name: Run pytest tests
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run: pytest tests -v
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run: pytest tests -v

‎.github/workflows/run-codecov.yml

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name: Run codecov
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on:
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push:
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branches: [dev]
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pull_request:
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branches: [master]
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jobs:
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pytest:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: [3.11]
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os: [ubuntu-latest]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install test dependencies
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run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
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- name: Install package
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run: python -m pip install .
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- name: Run pytest tests
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run: pytest tests --cov=./ --cov-report=xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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with:
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file: ./coverage.xml
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name: py-${{ matrix.python-version }}-${{ matrix.os }}

‎README.md

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@@ -2,6 +2,7 @@
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[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pepkit.github.io)
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![Run pytests](https://github.com/pepkit/pephubclient/workflows/Run%20pytests/badge.svg)
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[![codecov](https://codecov.io/gh/pepkit/pephubclient/branch/dev/graph/badge.svg)](https://codecov.io/gh/pepkit/pephubclient)
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[![pypi-badge](https://img.shields.io/pypi/v/pephubclient)](https://pypi.org/project/pephubclient)
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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‎codecov.yml

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ignore:
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- "*/cli.py"
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- "*/__main__.py"
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- "*/__init__.py"
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- "setup.py"

‎docs/changelog.md

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@@ -2,7 +2,9 @@
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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.
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5-
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## [0.1.1] - 2023-07-29
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### Fixed
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- New raw PEP structure was broken. ([#20](https://github.com/pepkit/pephubclient/issues/20))
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## [0.1.0] - 2023-04-16
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### Added

‎pephubclient/__init__.py

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@@ -1,7 +1,7 @@
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from pephubclient.pephubclient import PEPHubClient
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__app_name__ = "pephubclient"
4-
__version__ = "0.1.0"
4+
__version__ = "0.1.1"
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__author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
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77

‎pephubclient/constants.py

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@@ -4,8 +4,8 @@
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import pydantic
55
from pydantic import BaseModel
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7-
PEPHUB_BASE_URL = "https://pephub.databio.org/"
8-
# PEPHUB_BASE_URL = "http://0.0.0.0:8000/"
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# PEPHUB_BASE_URL = "https://pephub.databio.org/"
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PEPHUB_BASE_URL = "http://0.0.0.0:8000/"
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PEPHUB_PEP_API_BASE_URL = f"{PEPHUB_BASE_URL}api/v1/projects/"
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PEPHUB_PUSH_URL = f"{PEPHUB_BASE_URL}api/v1/namespaces/{{namespace}}/projects/json"
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‎pephubclient/helpers.py

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@@ -82,3 +82,5 @@ def call_client_func(func: Callable[..., Any], **kwargs) -> Any:
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MessageHandler.print_error(f"{err}")
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except PEPExistsError as err:
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MessageHandler.print_warning(f"PEP already exists. {err}")
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except OSError as err:
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MessageHandler.print_error(f"{err}")

‎pephubclient/models.py

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@@ -2,18 +2,17 @@
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33
import pydantic
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from pydantic import BaseModel, Extra, Field
5+
from peppy.const import CONFIG_KEY, SUBSAMPLE_RAW_LIST_KEY, SAMPLE_RAW_DICT_KEY
56

67

78
class ProjectDict(BaseModel):
89
"""
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Project dict (raw) model
1011
"""
1112

12-
description: Optional[str] = ""
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config: dict = Field(alias="_config")
14-
subsample_dict: Optional[list] = Field(alias="_subsample_dict")
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name: str
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sample_dict: dict = Field(alias="_sample_dict")
13+
config: dict = Field(alias=CONFIG_KEY)
14+
subsample_list: Optional[list] = Field(alias=SUBSAMPLE_RAW_LIST_KEY)
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sample_list: list = Field(alias=SAMPLE_RAW_DICT_KEY)
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class Config:
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allow_population_by_field_name = True

‎pephubclient/pephubclient.py

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@@ -4,6 +4,7 @@
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import pandas as pd
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import peppy
7+
from peppy.const import NAME_KEY, DESC_KEY, CONFIG_KEY
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import requests
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import urllib3
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from pydantic.error_wrappers import ValidationError
@@ -145,7 +146,10 @@ def upload(
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project["name"] = name
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upload_data = ProjectUploadData(
148-
pep_dict=project.to_dict(extended=True),
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pep_dict=project.to_dict(
150+
extended=True,
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orient="records",
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),
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tag=tag,
150154
is_private=is_private,
151155
overwrite=force,
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167171
)
168172
elif pephub_response.status_code == ResponseStatusCodes.UNAUTHORIZED:
169173
raise ResponseError("Unauthorized! Failure in uploading project.")
174+
elif pephub_response.status_code == ResponseStatusCodes.FORBIDDEN:
175+
raise ResponseError(
176+
"User does not have permission to write to this namespace!"
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)
170178
else:
171179
raise ResponseError("Unexpected Response Error.")
172180
return None
@@ -190,7 +198,7 @@ def _save_raw_pep(
190198
def full_path(fn: str) -> str:
191199
return os.path.join(folder_path, fn)
192200

193-
project_name = project_dict["name"]
201+
project_name = project_dict[CONFIG_KEY][NAME_KEY]
194202
sample_table_filename = "sample_table.csv"
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yaml_full_path = full_path(f"{project_name}_config.yaml")
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sample_full_path = full_path(sample_table_filename)
@@ -203,9 +211,9 @@ def full_path(fn: str) -> str:
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f"{len(extant)} file(s) exist(s): {', '.join(extant)}"
204212
)
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206-
config_dict = project_dict.get("_config")
207-
config_dict["name"] = project_name
208-
config_dict["description"] = project_dict["description"]
214+
config_dict = project_dict.get(CONFIG_KEY)
215+
config_dict[NAME_KEY] = project_name
216+
config_dict[DESC_KEY] = project_dict[CONFIG_KEY][DESC_KEY]
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config_dict["sample_table"] = sample_table_filename
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211219
sample_pandas = pd.DataFrame(project_dict.get("_sample_dict", {}))
@@ -251,6 +259,8 @@ def _load_raw_pep(
251259
:param jwt_data: JWT token.
252260
:return: Raw project in dict.
253261
"""
262+
if not jwt_data:
263+
jwt_data = FilesManager.load_jwt_data_from_file(self.PATH_TO_FILE_WITH_JWT)
254264
query_param = query_param or {}
255265
query_param["raw"] = "true"
256266

@@ -271,7 +281,9 @@ def _load_raw_pep(
271281
if pephub_response.status_code == ResponseStatusCodes.NOT_EXIST:
272282
raise ResponseError("File does not exist, or you are unauthorized.")
273283
if pephub_response.status_code == ResponseStatusCodes.INTERNAL_ERROR:
274-
raise ResponseError("Internal server error.")
284+
raise ResponseError(
285+
f"Internal server error. Unexpected return value. Error: {pephub_response.status_code}"
286+
)
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276288
def _set_registry_data(self, query_string: str) -> None:
277289
"""

‎requirements/requirements-all.txt

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typer>=0.7.0
2-
peppy>=0.35.4
2+
peppy>=0.35.7
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requests>=2.28.2
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pydantic>=1.10.6
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pydantic<2.0
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pandas>=2.0.0

‎requirements/requirements-test.txt

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pytest
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python-dotenv
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pytest-mock
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flake8
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flake8
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coveralls
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pytest-cov

‎tests/conftest.py

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@@ -17,19 +17,17 @@ def device_code_return():
1717
@pytest.fixture()
1818
def test_raw_pep_return():
1919
sample_prj = {
20-
"description": None,
21-
"config": {"This": "is config"},
22-
"subsample_dict": [],
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"name": "sample name",
24-
"sample_dict": {
25-
"organism": {"0": "pig", "1": "pig", "2": "frog", "3": "frog"},
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"sample_name": {
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"0": "pig_0h",
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"1": "pig_1h",
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"2": "frog_0h",
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"3": "frog_1h",
31-
},
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"config": {
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"This": "is config",
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"description": "desc",
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"name": "sample name",
3224
},
25+
"subsample_list": [],
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"sample_list": [
27+
{"time": "0", "file_path": "source1", "sample_name": "pig_0h"},
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{"time": "1", "file_path": "source1", "sample_name": "pig_1h"},
29+
{"time": "0", "file_path": "source1", "sample_name": "frog_0h"},
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],
3331
}
3432
return json.dumps(sample_prj)
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‎tests/test_pephubclient.py

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),
8888
(
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500,
90-
"Internal server error.",
90+
"Internal server error. Unexpected return value. Error: 500",
9191
),
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],
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)

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