Merge pull request #147 from pepkit/dev

Release 0.11.1

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.
 
+## [0.11.1] -- 2024-09-04
+- Added archive table of namespaces
+- Added sort by stars
+
 ## [0.11.0] -- 2024-07-24
 - Added validation schemas
 

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.11.0"
+__version__ = "0.11.1"

pepdbagent/db_utils.py

@@ -364,6 +364,30 @@ class SchemaGroupRelations(Base):
     )
 
 
+class TarNamespace(Base):
+
+    __tablename__ = "namespace_archives"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    namespace: Mapped[str] = mapped_column(ForeignKey("users.namespace", ondelete="CASCADE"))
+    file_path: Mapped[str] = mapped_column(nullable=False)
+    creation_date: Mapped[datetime.datetime] = mapped_column(default=deliver_update_date)
+    number_of_projects: Mapped[int] = mapped_column(default=0)
+    file_size: Mapped[int] = mapped_column(nullable=False)
+
+
+class BedBaseStats(Base):
+    __tablename__ = "bedbase_stats"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    gse: Mapped[str] = mapped_column()
+    gsm: Mapped[str] = mapped_column()
+    sample_name: Mapped[str] = mapped_column(nullable=True)
+    genome: Mapped[Optional[str]] = mapped_column(nullable=True, default="")
+    last_update_date: Mapped[Optional[str]] = mapped_column()
+    submission_date: Mapped[Optional[str]] = mapped_column()
+
+
 class BaseEngine:
     """
     A class with base methods, that are used in several classes. e.g. fetch_one or fetch_all

pepdbagent/models.py

@@ -280,7 +280,7 @@ class SchemaGroupAnnotation(BaseModel):
 
     namespace: str
     name: str
-    description: Optional[str]
+    description: Optional[str] = ""
     schemas: List[SchemaAnnotation]
 
 
@@ -293,3 +293,25 @@ class SchemaGroupSearchResult(BaseModel):
     limit: int
     offset: int
     results: List[SchemaGroupAnnotation]
+
+
+class TarNamespaceModel(BaseModel):
+    """
+    Namespace archive model
+    """
+
+    identifier: int = None
+    namespace: str
+    file_path: str
+    creation_date: datetime.datetime = None
+    number_of_projects: int = 0
+    file_size: int = 0
+
+
+class TarNamespaceModelReturn(BaseModel):
+    """
+    Namespace archive search model
+    """
+
+    count: int
+    results: List[TarNamespaceModel]

pepdbagent/modules/annotation.py

@@ -300,7 +300,7 @@ def _get_projects(
         :param limit: limit of return results
         :param offset: number of results off set (that were already showed)
         :param order_by: sort the result-set by the information
-            Options: ["name", "update_date", "submission_date"]
+            Options: ["update_date", "name",  "submission_date", "stars"]
             [Default: "update_date"]
         :param order_desc: Sort the records in descending order. [Default: False]
         :param filter_by: data to use filter on.
@@ -371,7 +371,7 @@ def _add_order_by_keyword(
 
         :param statement: sqlalchemy representation of a SELECT statement.
         :param by: sort the result-set by the information
-            Options: ["name", "update_date", "submission_date"]
+            Options: ["name", "update_date", "submission_date", "stars"]
             [Default: "update_date"]
         :param desc: Sort the records in descending order. [Default: False]
         :return: sqlalchemy representation of a SELECT statement with order by keyword
@@ -382,6 +382,8 @@ def _add_order_by_keyword(
             order_by_obj = Projects.name
         elif by == SUBMISSION_DATE_KEY:
             order_by_obj = Projects.submission_date
+        elif by == "stars":
+            order_by_obj = Projects.number_of_stars
         else:
             _LOGGER.warning(
                 f"order by: '{by}' statement is unavailable. Projects are sorted by 'update_date'"
@@ -614,7 +616,7 @@ def get_projects_list(
         :param limit: limit of return results
         :param offset: number of results off set (that were already showed)
         :param order_by: sort the result-set by the information
-            Options: ["name", "update_date", "submission_date"]
+            Options: ["name", "update_date", "submission_date", "stars"]
             [Default: "update_date"]
         :param order_desc: Sort the records in descending order. [Default: False]
         :param filter_by: data to use filter on.

pepdbagent/modules/namespace.py

@@ -3,19 +3,21 @@
 from datetime import datetime, timedelta
 from typing import List, Tuple, Union
 
-from sqlalchemy import distinct, func, or_, select
+from sqlalchemy import distinct, func, or_, select, delete
 from sqlalchemy.orm import Session
 from sqlalchemy.sql.selectable import Select
 
 from pepdbagent.const import DEFAULT_LIMIT, DEFAULT_LIMIT_INFO, DEFAULT_OFFSET, PKG_NAME
-from pepdbagent.db_utils import BaseEngine, Projects, User
+from pepdbagent.db_utils import BaseEngine, Projects, User, TarNamespace
 from pepdbagent.exceptions import NamespaceNotFoundError
 from pepdbagent.models import (
     ListOfNamespaceInfo,
     Namespace,
     NamespaceInfo,
     NamespaceList,
     NamespaceStats,
+    TarNamespaceModel,
+    TarNamespaceModelReturn,
 )
 from pepdbagent.utils import tuple_converter
 
@@ -300,3 +302,73 @@ def stats(self, namespace: str = None, monthly: bool = False) -> NamespaceStats:
             projects_updated=counts_last_update,
             projects_created=counts_submission,
         )
+
+    def upload_tar_info(self, tar_info: TarNamespaceModel) -> None:
+        """
+        Upload metadata of tar GEO files
+
+        tar_info: TarNamespaceModel
+        :return: None
+        """
+
+        with Session(self._sa_engine) as session:
+            new_tar = TarNamespace(
+                file_path=tar_info.file_path,
+                namespace=tar_info.namespace,
+                creation_date=tar_info.creation_date,
+                number_of_projects=tar_info.number_of_projects,
+                file_size=tar_info.file_size,
+            )
+            session.add(new_tar)
+            session.commit()
+
+            _LOGGER.info("Geo tar info was uploaded successfully!")
+
+    def get_tar_info(self, namespace: str) -> TarNamespaceModelReturn:
+        """
+        Get metadata of tar GEO files
+
+        :param namespace: namespace of the tar files
+
+        :return: list with geo data
+        """
+
+        with Session(self._sa_engine) as session:
+            tar_info = session.scalars(
+                select(TarNamespace)
+                .where(TarNamespace.namespace == namespace)
+                .order_by(TarNamespace.creation_date.desc())
+            )
+
+            results = []
+            for result in tar_info:
+                results.append(
+                    TarNamespaceModel(
+                        identifier=result.id,
+                        namespace=result.namespace,
+                        file_path=result.file_path,
+                        creation_date=result.creation_date,
+                        number_of_projects=result.number_of_projects,
+                        file_size=result.file_size,
+                    )
+                )
+
+        return TarNamespaceModelReturn(count=len(results), results=results)
+
+    def delete_tar_info(self, namespace: str = None) -> None:
+        """
+        Delete all metadata of tar GEO files
+
+        :param namespace: namespace of the tar files
+
+        :return: None
+        """
+
+        with Session(self._sa_engine) as session:
+
+            delete_statement = delete(TarNamespace)
+            if namespace:
+                delete_statement = delete_statement.where(TarNamespace.namespace == namespace)
+            session.execute(delete_statement)
+            session.commit()
+            _LOGGER.info("Geo tar info was deleted successfully!")

pepdbagent/modules/project.py

@@ -33,6 +33,7 @@
     Samples,
     Schemas,
     Subsamples,
+    TarNamespace,
     UpdateTypes,
     User,
 )
@@ -46,6 +47,8 @@
     SchemaDoesNotExistError,
 )
 from pepdbagent.models import (
+    TarNamespaceModel,
+    TarNamespaceModelReturn,
     HistoryAnnotationModel,
     HistoryChangeModel,
     ProjectDict,
@@ -657,6 +660,7 @@ def update(
                         ),
                         history_sa_model=new_history,
                     )
+                    found_prj.number_of_samples = len(update_dict["samples"])
 
                 if "subsamples" in update_dict:
                     if found_prj.subsamples_mapping:
@@ -1412,7 +1416,7 @@ def restore(
 
     def clean_history(self, days: int = 90) -> None:
         """
-        Delete all history data that is older then 3 month, or specific number of days
+        Delete all history data that is older than 3 month, or specific number of days
 
         :param days: number of days to keep history data
         :return: None

requirements/requirements-all.txt

@@ -1,6 +1,6 @@
 sqlalchemy>=2.0.0
 logmuse>=0.2.7
-peppy>=0.40.4
+peppy>=0.40.6
 ubiquerg>=0.6.2
 coloredlogs>=15.0.1
 pytest-mock

tests/test_tar_meta.py

@@ -0,0 +1,49 @@
+from datetime import datetime
+
+import pytest
+
+from pepdbagent.models import TarNamespaceModel
+
+from .utils import PEPDBAgentContextManager
+
+
+@pytest.mark.skipif(
+    not PEPDBAgentContextManager().db_setup(),
+    reason="DB is not setup",
+)
+class TestGeoTar:
+    """
+    Test project methods
+    """
+
+    test_namespace = "namespace1"
+
+    tar_info = TarNamespaceModel(
+        namespace=test_namespace,
+        submission_date=datetime.now(),
+        start_period=datetime.now(),
+        end_period=datetime.now(),
+        number_of_projects=1,
+        file_path="blabla/test.tar",
+    )
+
+    def test_create_meta_tar(self):
+        with PEPDBAgentContextManager(add_data=True) as agent:
+
+            agent.namespace.upload_tar_info(tar_info=self.tar_info)
+
+            result = agent.namespace.get_tar_info(namespace=self.test_namespace)
+
+            assert result.count == 1
+
+    def test_delete_meta_tar(self):
+        with PEPDBAgentContextManager(add_data=True) as agent:
+            agent.namespace.upload_tar_info(tar_info=self.tar_info)
+
+            result = agent.namespace.get_tar_info(namespace=self.test_namespace)
+            assert result.count == 1
+
+            agent.namespace.delete_tar_info()
+
+            result = agent.namespace.get_tar_info(namespace=self.test_namespace)
+            assert result.count == 0