Merge pull request #96 from pepkit/dev

Release v0.5.4

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.
 
+## [0.5.4] -- 2023-07-14
+- Added namespaces info method that returns list of namespaces with 
+
 ## [0.5.3] -- 2023-07-13
 - Fixed bugs in updating dates and descriptions
 

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.5.3"
+__version__ = "0.5.4"

pepdbagent/const.py

@@ -13,3 +13,5 @@
 
 # db_dialects
 POSTGRES_DIALECT = "postgresql"
+
+DEFAULT_LIMIT_INFO = 5

pepdbagent/models.py

@@ -130,3 +130,22 @@ def value_should_not_contain_question(cls, v):
     class Config:
         extra = Extra.forbid
         allow_population_by_field_name = True
+
+
+class NamespaceInfo(BaseModel):
+    """
+    Model with information about namespace
+    """
+
+    namespace: str
+    number_of_projects: int
+
+
+class ListOfNamespaceInfo(BaseModel):
+    """
+    Namespace information response model
+    """
+
+    number_of_namespaces: int
+    limit: int
+    results: List[NamespaceInfo]

pepdbagent/modules/namespace.py

@@ -1,13 +1,13 @@
 import logging
 from typing import List, Union
 
-from sqlalchemy import distinct, func, or_, select
+from sqlalchemy import distinct, func, or_, select, text
 from sqlalchemy.sql.selectable import Select
 from sqlalchemy.orm import Session
 
-from pepdbagent.const import DEFAULT_LIMIT, DEFAULT_OFFSET, PKG_NAME
+from pepdbagent.const import DEFAULT_LIMIT, DEFAULT_OFFSET, PKG_NAME, DEFAULT_LIMIT_INFO
 from pepdbagent.db_utils import Projects, BaseEngine
-from pepdbagent.models import Namespace, NamespaceList
+from pepdbagent.models import Namespace, NamespaceList, NamespaceInfo, ListOfNamespaceInfo
 from pepdbagent.utils import tuple_converter
 
 _LOGGER = logging.getLogger(PKG_NAME)
@@ -71,6 +71,7 @@ def _get_namespace(
     ) -> List[Namespace]:
         """
         Search for namespace by providing search string.
+
         :param search_str: string of symbols, words, keywords to search in the
             namespace name.
         :param admin_nsp: tuple of namespaces where project can be retrieved if they are privet
@@ -114,9 +115,10 @@ def _get_namespace(
             )
         return results_list
 
-    def _count_namespace(self, search_str: str = None, admin_nsp: tuple = None) -> int:
+    def _count_namespace(self, search_str: str = None, admin_nsp: tuple = tuple()) -> int:
         """
         Get number of found namespace. [This function is related to _get_namespaces]
+
         :param search_str: string of symbols, words, keywords to search in the
             namespace name.
         :param admin_nsp: tuple of namespaces where project can be retrieved if they are privet
@@ -160,3 +162,45 @@ def _add_condition(
             or_(Projects.private.is_(False), Projects.namespace.in_(admin_list))
         )
         return statement
+
+    def info(self, limit: int = DEFAULT_LIMIT_INFO) -> ListOfNamespaceInfo:
+        """
+        Get list of top n namespaces in the database
+
+        :param limit: limit of results (top namespace )
+        :return: number_of_namespaces: int
+                 limit: int
+                 results: { namespace: str
+                            number_of_projects: int
+                            }
+        """
+        total_number_of_namespaces = self._count_namespace()
+
+        statement = (
+            select(
+                func.count(Projects.namespace).label("number_of_projects"),
+                Projects.namespace,
+            )
+            .select_from(Projects)
+            .where(Projects.private.is_(False))
+            .limit(limit)
+            .order_by(text("number_of_projects desc"))
+            .group_by(Projects.namespace)
+        )
+
+        with Session(self._sa_engine) as session:
+            query_results = session.execute(statement).all()
+
+        list_of_results = []
+        for result in query_results:
+            list_of_results.append(
+                NamespaceInfo(
+                    namespace=result.namespace,
+                    number_of_projects=result.number_of_projects,
+                )
+            )
+        return ListOfNamespaceInfo(
+            number_of_namespaces=total_number_of_namespaces,
+            limit=limit,
+            results=list_of_results,
+        )

pepdbagent/modules/project.py

@@ -350,11 +350,12 @@ def _overwrite(
                     found_prj.pep_schema = pep_schema
                     found_prj.config = project_dict[CONFIG_KEY]
                     found_prj.description = description
+                    found_prj.last_update_date = datetime.datetime.now(datetime.timezone.utc)
 
                     # Deleting old samples and subsamples
                     if found_prj.samples_mapping:
                         for sample in found_prj.samples_mapping:
-                            _LOGGER.info(f"deleting samples: {str(sample)}")
+                            _LOGGER.debug(f"deleting samples: {str(sample)}")
                             session.delete(sample)
 
                     if found_prj.subsamples_mapping:

tests/test_pepagent.py

@@ -410,3 +410,14 @@ def test_annotation(self, initiate_pepdb_con):
     def test_annotation_private(self, initiate_pepdb_con):
         result = initiate_pepdb_con.namespace.get(admin="private_test")
         assert len(result.results) == 4
+
+    def test_namespace_info(self, initiate_pepdb_con):
+        initiate_pepdb_con.project.update(
+            namespace="private_test",
+            name="derive",
+            tag="default",
+            update_dict={"is_private": False},
+        )
+        result = initiate_pepdb_con.namespace.info()
+        assert len(result.results) == 4
+        assert result.results[3].number_of_projects == 1