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fixed #33
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@khoroshevskyi
khoroshevskyi committed Jan 22, 2024
1 parent fae2fb5 commit 12b578a
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Showing 2 changed files with 97 additions and 81 deletions.
72 changes: 72 additions & 0 deletions pephubclient/helpers.py
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,14 @@
import json
from typing import Any, Callable, Optional
import os
import pandas as pd
from peppy.const import (
NAME_KEY,
DESC_KEY,
CONFIG_KEY,
SUBSAMPLE_RAW_LIST_KEY,
SAMPLE_RAW_DICT_KEY,
)

import requests
from requests.exceptions import ConnectionError
Expand All @@ -9,6 +18,7 @@

from pephubclient.exceptions import PEPExistsError, ResponseError
from pephubclient.constants import RegistryPath
from pephubclient.files_manager import FilesManager


class RequestManager:
Expand Down Expand Up @@ -103,3 +113,65 @@ def is_registry_path(input_string: str) -> bool:
except (ValidationError, TypeError):
return False
return True


def save_raw_pep(
reg_path: str,
project_dict: dict,
force: bool = False,
) -> None:
"""
Save project locally.
:param dict project_dict: PEP dictionary (raw project)
:param bool force: overwrite project if exists
:return: None
"""
reg_path_model = RegistryPath(**parse_registry_path(reg_path))
folder_path = FilesManager.create_project_folder(registry_path=reg_path_model)

def full_path(fn: str) -> str:
return os.path.join(folder_path, fn)

project_name = project_dict[CONFIG_KEY][NAME_KEY]
sample_table_filename = "sample_table.csv"
yaml_full_path = full_path(f"{project_name}_config.yaml")
sample_full_path = full_path(sample_table_filename)
if not force:
extant = [p for p in [yaml_full_path, sample_full_path] if os.path.isfile(p)]
if extant:
raise PEPExistsError(f"{len(extant)} file(s) exist(s): {', '.join(extant)}")

config_dict = project_dict.get(CONFIG_KEY)
config_dict[NAME_KEY] = project_name
config_dict[DESC_KEY] = project_dict[CONFIG_KEY][DESC_KEY]
config_dict["sample_table"] = sample_table_filename

sample_pandas = pd.DataFrame(project_dict.get(SAMPLE_RAW_DICT_KEY, {}))

subsample_list = [
pd.DataFrame(sub_a) for sub_a in project_dict.get(SUBSAMPLE_RAW_LIST_KEY) or []
]

filenames = []
for idx, subsample in enumerate(subsample_list):
fn = f"subsample_table{idx + 1}.csv"
filenames.append(fn)
FilesManager.save_pandas(subsample, full_path(fn), not_force=False)
config_dict["subsample_table"] = filenames

FilesManager.save_yaml(config_dict, yaml_full_path, not_force=False)
FilesManager.save_pandas(sample_pandas, sample_full_path, not_force=False)

if config_dict.get("subsample_table"):
for number, subsample in enumerate(subsample_list):
FilesManager.save_pandas(
subsample,
os.path.join(folder_path, config_dict["subsample_table"][number]),
not_force=False,
)

MessageHandler.print_success(
f"Project was downloaded successfully -> {folder_path}"
)
return None
106 changes: 25 additions & 81 deletions pephubclient/pephubclient.py
View file
Original file line number Diff line number Diff line change
@@ -1,16 +1,10 @@
import json
import os
from typing import NoReturn, Optional, Literal
from typing_extensions import deprecated

import pandas as pd
import peppy
from peppy.const import (
NAME_KEY,
DESC_KEY,
CONFIG_KEY,
SUBSAMPLE_RAW_LIST_KEY,
SAMPLE_RAW_DICT_KEY,
)
from peppy.const import NAME_KEY
import requests
import urllib3
from pydantic import ValidationError
Expand All @@ -25,11 +19,10 @@
)
from pephubclient.exceptions import (
IncorrectQueryStringError,
PEPExistsError,
ResponseError,
)
from pephubclient.files_manager import FilesManager
from pephubclient.helpers import MessageHandler, RequestManager
from pephubclient.helpers import MessageHandler, RequestManager, save_raw_pep
from pephubclient.models import (
ProjectDict,
ProjectUploadData,
Expand Down Expand Up @@ -76,11 +69,11 @@ def pull(self, project_registry_path: str, force: Optional[bool] = False) -> Non
:return: None
"""
jwt_data = FilesManager.load_jwt_data_from_file(self.PATH_TO_FILE_WITH_JWT)
project_dict = self._load_raw_pep(
project_dict = self.load_raw_pep(
registry_path=project_registry_path, jwt_data=jwt_data
)

self._save_raw_pep(
save_raw_pep(
reg_path=project_registry_path, project_dict=project_dict, force=force
)

Expand All @@ -97,7 +90,7 @@ def load_project(
:return Project: peppy project.
"""
jwt = FilesManager.load_jwt_data_from_file(self.PATH_TO_FILE_WITH_JWT)
raw_pep = self._load_raw_pep(project_registry_path, jwt, query_param)
raw_pep = self.load_raw_pep(project_registry_path, jwt, query_param)
peppy_project = peppy.Project().from_dict(raw_pep)
return peppy_project

Expand Down Expand Up @@ -247,80 +240,32 @@ def find_project(
project_list.append(ProjectAnnotationModel(**project_found))
return SearchReturnModel(**json.loads(decoded_response))

@staticmethod
def _save_raw_pep(
reg_path: str,
project_dict: dict,
force: bool = False,
) -> None:
@deprecated("This method is deprecated. Use load_raw_pep instead.")
def _load_raw_pep(
self,
registry_path: str,
jwt_data: Optional[str] = None,
query_param: Optional[dict] = None,
) -> dict:
"""
Save project locally.
!!! This method is deprecated. Use load_raw_pep instead. !!!
:param dict project_dict: PEP dictionary (raw project)
:param bool force: overwrite project if exists
:return: None
Request PEPhub and return the requested project as peppy.Project object.
:param registry_path: Project namespace, eg. "geo/GSE124224:tag"
:param query_param: Optional variables to be passed to PEPhub
:param jwt_data: JWT token.
:return: Raw project in dict.
"""
reg_path_model = RegistryPath(**parse_registry_path(reg_path))
folder_path = FilesManager.create_project_folder(registry_path=reg_path_model)

def full_path(fn: str) -> str:
return os.path.join(folder_path, fn)

project_name = project_dict[CONFIG_KEY][NAME_KEY]
sample_table_filename = "sample_table.csv"
yaml_full_path = full_path(f"{project_name}_config.yaml")
sample_full_path = full_path(sample_table_filename)
if not force:
extant = [
p for p in [yaml_full_path, sample_full_path] if os.path.isfile(p)
]
if extant:
raise PEPExistsError(
f"{len(extant)} file(s) exist(s): {', '.join(extant)}"
)

config_dict = project_dict.get(CONFIG_KEY)
config_dict[NAME_KEY] = project_name
config_dict[DESC_KEY] = project_dict[CONFIG_KEY][DESC_KEY]
config_dict["sample_table"] = sample_table_filename

sample_pandas = pd.DataFrame(project_dict.get(SAMPLE_RAW_DICT_KEY, {}))

subsample_list = [
pd.DataFrame(sub_a)
for sub_a in project_dict.get(SUBSAMPLE_RAW_LIST_KEY) or []
]

filenames = []
for idx, subsample in enumerate(subsample_list):
fn = f"subsample_table{idx + 1}.csv"
filenames.append(fn)
FilesManager.save_pandas(subsample, full_path(fn), not_force=False)
config_dict["subsample_table"] = filenames

FilesManager.save_yaml(config_dict, yaml_full_path, not_force=False)
FilesManager.save_pandas(sample_pandas, sample_full_path, not_force=False)

if config_dict.get("subsample_table"):
for number, subsample in enumerate(subsample_list):
FilesManager.save_pandas(
subsample,
os.path.join(folder_path, config_dict["subsample_table"][number]),
not_force=False,
)

MessageHandler.print_success(
f"Project was downloaded successfully -> {folder_path}"
)
return None
return self.load_raw_pep(registry_path, jwt_data, query_param)

def _load_raw_pep(
def load_raw_pep(
self,
registry_path: str,
jwt_data: Optional[str] = None,
query_param: Optional[dict] = None,
) -> dict:
"""project_name
"""
Request PEPhub and return the requested project as peppy.Project object.
:param registry_path: Project namespace, eg. "geo/GSE124224:tag"
Expand Down Expand Up @@ -396,9 +341,8 @@ def _build_pull_request_url(self, query_param: dict = None) -> str:

return PEPHUB_PEP_API_BASE_URL + endpoint

def _build_project_search_url(
self, namespace: str, query_param: dict = None
) -> str:
@staticmethod
def _build_project_search_url(namespace: str, query_param: dict = None) -> str:
"""
Build request for searching projects form pephub
Expand Down

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