Merge pull request #136 from pepkit/133_tests

133 tests

docs/changelog.md

@@ -2,6 +2,12 @@
 
 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.
 
+## [0.9.0] -- 2024-06-25
+- Introduced new sample ordering with linked list [#133](https://github.com/pepkit/pepdbagent/issues/133)
+- Efficiency improvements of project update function 
+- Test restructuring 
+
+
 ## [0.8.0] -- 2024-02-26
 - Fixed forking schema
 - Improved forking efficiency [#129](https://github.com/pepkit/pepdbagent/issues/129)

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.8.0"
+__version__ = "0.9.0"

pepdbagent/db_utils.py

@@ -324,3 +324,15 @@ def check_db_connection(self):
             self.session_execute(select(Projects).limit(1))
         except ProgrammingError:
             raise SchemaError()
+
+    def delete_schema(self, engine=None) -> None:
+        """
+        Delete sql schema in the database.
+
+        :param engine: sqlalchemy engine [Default: None]
+        :return: None
+        """
+        if not engine:
+            engine = self._engine
+        Base.metadata.drop_all(engine)
+        return None

pepdbagent/modules/project.py

@@ -132,7 +132,7 @@ def _get_samples(self, session: Session, prj_id: int, with_id: bool) -> List[Dic
         for sample in samples_results:
             sample_dict = sample.sample
             if with_id:
-                sample_dict["ph_id"] = sample.guid
+                sample_dict[PEPHUB_SAMPLE_ID_KEY] = sample.guid
 
             result_dict[sample.guid] = {
                 "sample": sample_dict,
@@ -477,6 +477,13 @@ def update(
                     is_private: Optional[bool]
                     tag: Optional[str]
                     name: Optional[str]
+                    description: Optional[str]
+                    is_private: Optional[bool]
+                    pep_schema: Optional[str]
+                    config: Optional[dict]
+                    samples: Optional[List[dict]]
+                    subsamples: Optional[List[List[dict]]]
+                    pop: Optional[bool]
             }
         :param namespace: project namespace
         :param name: project name

pepdbagent/pepdbagent.py

@@ -45,47 +45,48 @@ def __init__(
         )
         sa_engine = pep_db_engine.engine
 
-        self.__sa_engine = sa_engine
+        self.pep_db_engine = pep_db_engine
+        self._sa_engine = sa_engine
 
-        self.__project = PEPDatabaseProject(pep_db_engine)
-        self.__annotation = PEPDatabaseAnnotation(pep_db_engine)
-        self.__namespace = PEPDatabaseNamespace(pep_db_engine)
-        self.__sample = PEPDatabaseSample(pep_db_engine)
-        self.__user = PEPDatabaseUser(pep_db_engine)
-        self.__view = PEPDatabaseView(pep_db_engine)
+        self._project = PEPDatabaseProject(pep_db_engine)
+        self._annotation = PEPDatabaseAnnotation(pep_db_engine)
+        self._namespace = PEPDatabaseNamespace(pep_db_engine)
+        self._sample = PEPDatabaseSample(pep_db_engine)
+        self._user = PEPDatabaseUser(pep_db_engine)
+        self._view = PEPDatabaseView(pep_db_engine)
 
-        self.__db_name = database
+        self._db_name = database
 
     @property
     def project(self) -> PEPDatabaseProject:
-        return self.__project
+        return self._project
 
     @property
     def annotation(self) -> PEPDatabaseAnnotation:
-        return self.__annotation
+        return self._annotation
 
     @property
     def namespace(self) -> PEPDatabaseNamespace:
-        return self.__namespace
+        return self._namespace
 
     @property
     def user(self) -> PEPDatabaseUser:
-        return self.__user
+        return self._user
 
     @property
     def sample(self) -> PEPDatabaseSample:
-        return self.__sample
+        return self._sample
 
     @property
     def view(self) -> PEPDatabaseView:
-        return self.__view
+        return self._view
 
     def __str__(self):
         return f"Connection to the database: '{self.__db_name}' is set!"
 
     def __exit__(self):
-        self.__sa_engine.__exit__()
+        self._sa_engine.__exit__()
 
     @property
     def connection(self):
-        return self.__sa_engine
+        return self._sa_engine

pepdbagent/utils.py

@@ -8,7 +8,7 @@
 import ubiquerg
 from peppy.const import SAMPLE_RAW_DICT_KEY
 
-from .exceptions import RegistryPathError
+from pepdbagent.exceptions import RegistryPathError
 
 
 def is_valid_registry_path(rpath: str) -> bool:
@@ -101,7 +101,7 @@ def convert_date_string_to_date(date_string: str) -> datetime.datetime:
     """
     Convert string into datetime format
 
-    :param date_str: date string in format [YYYY/MM/DD]. e.g. 2022/02/22
+    :param date_string: date string in format [YYYY/MM/DD]. e.g. 2022/02/22
     :return: datetime format
     """
     return datetime.datetime.strptime(date_string, "%Y/%m/%d") + datetime.timedelta(days=1)
@@ -111,6 +111,8 @@ def order_samples(results: dict) -> List[dict]:
     """
     Order samples by their parent_guid
 
+    # TODO: To make this function more efficient, we should write it in Rust!
+
     :param results: dictionary of samples. Structure: {
                             "sample": sample_dict,
                             "guid": sample.guid,

tests/conftest.py

@@ -1,83 +1,83 @@
-import os
-
-import peppy
-import pytest
-from sqlalchemy import create_engine, text
-
-from pepdbagent import PEPDatabaseAgent
-
-DNS = "postgresql+psycopg://postgres:docker@localhost:5432/pep-db"
-
-
-DATA_PATH = os.path.join(
-    os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
-    "tests",
-    "data",
-)
-
-
-def get_path_to_example_file(namespace, project_name):
-    return os.path.join(DATA_PATH, namespace, project_name, "project_config.yaml")
-
-
-@pytest.fixture
-def list_of_available_peps():
-    pep_namespaces = os.listdir(DATA_PATH)
-    projects = {}
-    for np in pep_namespaces:
-        pep_name = os.listdir(os.path.join(DATA_PATH, np))
-        projects[np] = {p: get_path_to_example_file(np, p) for p in pep_name}
-    return projects
-
-
-@pytest.fixture(scope="function")
-def initiate_pepdb_con(
-    list_of_available_peps,
-):
-    sa_engine = create_engine(DNS)
-    with sa_engine.begin() as conn:
-        conn.execute(text("DROP table IF EXISTS projects CASCADE"))
-        conn.execute(text("DROP table IF EXISTS samples CASCADE"))
-        conn.execute(text("DROP table IF EXISTS subsamples CASCADE"))
-        conn.execute(text("DROP table IF EXISTS stars CASCADE"))
-        conn.execute(text("DROP table IF EXISTS users CASCADE"))
-        conn.execute(text("DROP table IF EXISTS views CASCADE"))
-        conn.execute(text("DROP table IF EXISTS views_samples CASCADE"))
-
-    pepdb_con = PEPDatabaseAgent(dsn=DNS, echo=True)
-    for namespace, item in list_of_available_peps.items():
-        if namespace == "private_test":
-            private = True
-        else:
-            private = False
-        for name, path in item.items():
-            prj = peppy.Project(path)
-            pepdb_con.project.create(
-                namespace=namespace,
-                name=name,
-                tag="default",
-                is_private=private,
-                project=prj,
-                overwrite=True,
-                pep_schema="random_schema_name",
-            )
-
-    yield pepdb_con
-
-
-@pytest.fixture(scope="function")
-def initiate_empty_pepdb_con(
-    list_of_available_peps,
-):
-    """
-    create connection without adding peps to the db
-    """
-    # sa_engine = create_engine(DNS)
-    # with sa_engine.begin() as conn:
-    #     conn.execute(text("DROP table IF EXISTS projects CASCADE"))
-    #     conn.execute(text("DROP table IF EXISTS samples CASCADE"))
-    #     conn.execute(text("DROP table IF EXISTS subsamples CASCADE"))
-
-    pepdb_con = PEPDatabaseAgent(dsn=DNS, echo=False)
-
-    yield pepdb_con
+# import os
+#
+# import peppy
+# import pytest
+# from sqlalchemy import create_engine, text
+#
+# from pepdbagent import PEPDatabaseAgent
+#
+# DNS = "postgresql+psycopg://postgres:docker@localhost:5432/pep-db"
+#
+#
+# DATA_PATH = os.path.join(
+#     os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
+#     "tests",
+#     "data",
+# )
+#
+#
+# def get_path_to_example_file(namespace, project_name):
+#     return os.path.join(DATA_PATH, namespace, project_name, "project_config.yaml")
+#
+#
+# @pytest.fixture
+# def list_of_available_peps():
+#     pep_namespaces = os.listdir(DATA_PATH)
+#     projects = {}
+#     for np in pep_namespaces:
+#         pep_name = os.listdir(os.path.join(DATA_PATH, np))
+#         projects[np] = {p: get_path_to_example_file(np, p) for p in pep_name}
+#     return projects
+#
+#
+# @pytest.fixture(scope="function")
+# def initiate_pepdb_con(
+#     list_of_available_peps,
+# ):
+#     sa_engine = create_engine(DNS)
+#     with sa_engine.begin() as conn:
+#         conn.execute(text("DROP table IF EXISTS projects CASCADE"))
+#         conn.execute(text("DROP table IF EXISTS samples CASCADE"))
+#         conn.execute(text("DROP table IF EXISTS subsamples CASCADE"))
+#         conn.execute(text("DROP table IF EXISTS stars CASCADE"))
+#         conn.execute(text("DROP table IF EXISTS users CASCADE"))
+#         conn.execute(text("DROP table IF EXISTS views CASCADE"))
+#         conn.execute(text("DROP table IF EXISTS views_samples CASCADE"))
+#
+#     pepdb_con = PEPDatabaseAgent(dsn=DNS, echo=True)
+#     for namespace, item in list_of_available_peps.items():
+#         if namespace == "private_test":
+#             private = True
+#         else:
+#             private = False
+#         for name, path in item.items():
+#             prj = peppy.Project(path)
+#             pepdb_con.project.create(
+#                 namespace=namespace,
+#                 name=name,
+#                 tag="default",
+#                 is_private=private,
+#                 project=prj,
+#                 overwrite=True,
+#                 pep_schema="random_schema_name",
+#             )
+#
+#     yield pepdb_con
+#
+#
+# @pytest.fixture(scope="function")
+# def initiate_empty_pepdb_con(
+#     list_of_available_peps,
+# ):
+#     """
+#     create connection without adding peps to the db
+#     """
+#     # sa_engine = create_engine(DNS)
+#     # with sa_engine.begin() as conn:
+#     #     conn.execute(text("DROP table IF EXISTS projects CASCADE"))
+#     #     conn.execute(text("DROP table IF EXISTS samples CASCADE"))
+#     #     conn.execute(text("DROP table IF EXISTS subsamples CASCADE"))
+#
+#     pepdb_con = PEPDatabaseAgent(dsn=DNS, echo=False)
+#
+#     yield pepdb_con