Merge pull request #25 from pepkit/dev

Release 0.2.0

Author: khoroshevskyi

codecov.yml

@@ -11,7 +11,7 @@ coverage:
       tests:
         paths:
           - "tests/"
-        target: 100%
+        target: 70%
       source:
         paths:
           - "jupytext/"

docs/changelog.md

@@ -2,6 +2,10 @@
 
 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.
 
+## [0.2.0] - 2023-10-02
+### Added
+- Project search functionality
+
 ## [0.1.1] - 2023-07-29
 ### Fixed
 - Incorrect base url

pephubclient/__init__.py

@@ -1,7 +1,7 @@
 from pephubclient.pephubclient import PEPHubClient
 
 __app_name__ = "pephubclient"
-__version__ = "0.1.2"
+__version__ = "0.2.0"
 __author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
 
 

pephubclient/constants.py

@@ -7,6 +7,7 @@
 PEPHUB_BASE_URL = "https://pephub.databio.org/"
 # PEPHUB_BASE_URL = "http://0.0.0.0:8000/"
 PEPHUB_PEP_API_BASE_URL = f"{PEPHUB_BASE_URL}api/v1/projects/"
+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"
 
 

pephubclient/models.py

@@ -1,4 +1,5 @@
-from typing import Optional
+import datetime
+from typing import Optional, List
 
 import pydantic
 from pydantic import BaseModel, Extra, Field
@@ -32,3 +33,23 @@ class ProjectUploadData(BaseModel):
     @pydantic.validator("tag")
     def tag_should_not_be_none(cls, v):
         return v or "default"
+
+
+class ProjectAnnotationModel(BaseModel):
+    namespace: str
+    name: str
+    tag: str
+    is_private: bool
+    number_of_samples: int
+    description: str
+    last_update_date: datetime.datetime
+    submission_date: datetime.datetime
+    digest: str
+    pep_schema: str
+
+
+class SearchReturnModel(BaseModel):
+    count: int
+    limit: int
+    offset: int
+    items: List[ProjectAnnotationModel]

pephubclient/pephubclient.py

@@ -1,6 +1,6 @@
 import json
 import os
-from typing import NoReturn, Optional
+from typing import NoReturn, Optional, Literal
 
 import pandas as pd
 import peppy
@@ -21,6 +21,7 @@
     PEPHUB_PUSH_URL,
     RegistryPath,
     ResponseStatusCodes,
+    PEPHUB_PEP_SEARCH_URL,
 )
 from pephubclient.exceptions import (
     IncorrectQueryStringError,
@@ -29,7 +30,12 @@
 )
 from pephubclient.files_manager import FilesManager
 from pephubclient.helpers import MessageHandler, RequestManager
-from pephubclient.models import ProjectDict, ProjectUploadData
+from pephubclient.models import (
+    ProjectDict,
+    ProjectUploadData,
+    SearchReturnModel,
+    ProjectAnnotationModel,
+)
 from pephubclient.pephub_oauth.pephub_oauth import PEPHubAuth
 
 urllib3.disable_warnings()
@@ -182,9 +188,65 @@ def upload(
                 "User does not have permission to write to this namespace!"
             )
         else:
-            raise ResponseError("Unexpected Response Error.")
+            raise ResponseError(
+                f"Unexpected Response Error. {pephub_response.status_code}"
+            )
         return None
 
+    def find_project(
+        self,
+        namespace: str,
+        query_string: str = "",
+        limit: int = 100,
+        offset: int = 0,
+        filter_by: Literal["submission_date", "last_update_date"] = None,
+        start_date: str = None,
+        end_date: str = None,
+    ) -> SearchReturnModel:
+        """
+        Find project in specific namespace and return list of PEP annotation
+
+        :param namespace: Namespace where to search for projects
+        :param query_string: Search query
+        :param limit: Return limit
+        :param offset: Return offset
+        :param filter_by: Use filter date. Option: [submission_date, last_update_date]
+        :param start_date: filter beginning date
+        :param end_date: filter end date (if none today's date is used)
+        :return:
+        """
+        jwt_data = FilesManager.load_jwt_data_from_file(self.PATH_TO_FILE_WITH_JWT)
+
+        query_param = {
+            "q": query_string,
+            "limit": limit,
+            "offset": offset,
+        }
+        if filter_by in ["submission_date", "last_update_date"]:
+            query_param["filter_by"] = filter_by
+            query_param["filter_start_date"] = start_date
+            if end_date:
+                query_param["filter_end_date"] = end_date
+
+        url = self._build_project_search_url(
+            namespace=namespace,
+            query_param=query_param,
+        )
+
+        pephub_response = self.send_request(
+            method="GET",
+            url=url,
+            headers=self._get_header(jwt_data),
+            json=None,
+            cookies=None,
+        )
+        if pephub_response.status_code == ResponseStatusCodes.OK:
+            decoded_response = self._handle_pephub_response(pephub_response)
+            project_list = []
+            for project_found in json.loads(decoded_response)["items"]:
+                project_list.append(ProjectAnnotationModel(**project_found))
+            return SearchReturnModel(**json.loads(decoded_response))
+
     @staticmethod
     def _save_raw_pep(
         reg_path: str,
@@ -334,6 +396,21 @@ 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:
+        """
+        Build request for searching projects form pephub
+
+        :param query_param: dict of parameters used in query string
+        :return: url string
+        """
+
+        variables_string = PEPHubClient._parse_query_param(query_param)
+        endpoint = variables_string
+
+        return PEPHUB_PEP_SEARCH_URL.format(namespace=namespace) + endpoint
+
     @staticmethod
     def _build_push_request_url(namespace: str) -> str:
         """

tests/test_pephubclient.py

@@ -147,3 +147,14 @@ def test_push_with_pephub_error_response(
                 namespace="s_name",
                 name="name",
             )
+
+    def test_search_prj(self, mocker):
+        return_value = b'{"count":1,"limit":100,"offset":0,"items":[{"namespace":"namespace1","name":"basic","tag":"default","is_private":false,"number_of_samples":2,"description":"None","last_update_date":"2023-08-27 19:07:31.552861+00:00","submission_date":"2023-08-27 19:07:31.552858+00:00","digest":"08cbcdbf4974fc84bee824c562b324b5","pep_schema":"random_schema_name"}],"session_info":null,"can_edit":false}'
+        requests_mock = mocker.patch(
+            "requests.request",
+            return_value=Mock(content=return_value, status_code=200),
+        )
+
+        return_value = PEPHubClient().find_project(namespace="namespace1")
+        assert return_value.count == 1
+        assert len(return_value.items) == 1