Release 0.11.1

docs/changelog.md

@@ -2,6 +2,9 @@
 
 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 metadata table for namespace tar files
+
 ## [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 +364,19 @@ class SchemaGroupRelations(Base):
     )
 
 
+class TarNamespace(Base):
+
+    __tablename__ = "tar_namespace"
+
+    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)
+    submission_date: Mapped[datetime.datetime] = mapped_column(default=deliver_update_date)
+    start_period: Mapped[datetime.datetime] = mapped_column(nullable=True)
+    end_period: Mapped[datetime.datetime] = mapped_column(nullable=True)
+    number_of_projects: Mapped[int] = mapped_column(default=0)
+
+
 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 +293,26 @@ class SchemaGroupSearchResult(BaseModel):
     limit: int
     offset: int
     results: List[SchemaGroupAnnotation]
+
+
+class TarNamespaceModel(BaseModel):
+    """
+    Geo project model
+    """
+
+    identifier: int = None
+    namespace: str
+    file_path: str
+    submission_date: datetime.datetime = None
+    start_period: datetime.datetime
+    end_period: datetime.datetime
+    number_of_projects: int = 0
+
+
+class TarNamespaceModelReturn(BaseModel):
+    """
+    Geo project model
+    """
+
+    count: int
+    results: List[TarNamespaceModel]

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 +302,74 @@ 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,
+                start_period=tar_info.start_period,
+                end_period=tar_info.end_period,
+                number_of_projects=tar_info.number_of_projects,
+            )
+            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.submission_date.desc())
+            )
+
+            results = []
+            for result in tar_info:
+                results.append(
+                    TarNamespaceModel(
+                        identifier=result.id,
+                        namespace=result.namespace,
+                        file_path=result.file_path,
+                        start_period=result.start_period,
+                        end_period=result.end_period,
+                        submission_date=result.submission_date,
+                        number_of_projects=result.number_of_projects,
+                    )
+                )
+
+        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

tests/test_tar_meta.py

@@ -0,0 +1,52 @@
+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
+            assert result.results[0].end_period.strftime(
+                "%Y:%m:%d"
+            ) == self.tar_info.end_period.strftime("%Y:%m:%d")
+
+    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