Merge pull request #46 from databio/dev

release 0.5.0

.github/workflows/cli-coverage.yml

@@ -16,8 +16,8 @@ jobs:
         image: postgres
         env:
           POSTGRES_USER: postgres
-          POSTGRES_PASSWORD: dockerpassword
-          POSTGRES_DB: pipestat-test
+          POSTGRES_PASSWORD: docker
+          POSTGRES_DB: bedbase
           POSTGRES_HOST: localhost
         ports:
           - 5432:5432

.github/workflows/run-pytest.yml

@@ -20,8 +20,8 @@ jobs:
           image: postgres
           env:
             POSTGRES_USER: postgres
-            POSTGRES_PASSWORD: dockerpassword
-            POSTGRES_DB: pipestat-test
+            POSTGRES_PASSWORD: docker
+            POSTGRES_DB: bedbase
             POSTGRES_HOST: localhost
           ports:
           - 5432:5432

MANIFEST.in

@@ -2,3 +2,6 @@ include README.md
 include LICENSE.txt
 include requirements/*
 include bbconf/schemas/*
+include bbconf/modules/*
+include bbconf/config_parser/*
+include bbconf/models/*

README.md

@@ -13,7 +13,7 @@
 ## What is this?
 
 `bbconf` is a configuration and management tool for BEDbase, facilitating the reading of configuration files, 
-setting up connections to PostgreSQL and Qdrant databases, managing file paths, and storing transformer models. 
+setting up connections to PostgreSQL, PEPhub, S3, and Qdrant databases, managing file paths, and storing transformer models. 
 It formalizes communication pathways for pipelines and downstream tools, ensuring seamless interaction."
 
 ---

bbconf/__init__.py

@@ -1,11 +1,13 @@
 import logging
+
 import coloredlogs
 
-from bbconf.bbconf import BedBaseConf, get_bedbase_cfg
+from bbconf.bbagent import BedBaseAgent
+
 from ._version import __version__
 from .const import PKG_NAME
 
-__all__ = ["BedBaseConf", "get_bedbase_cfg", "__version__"]
+__all__ = ["BedBaseAgent", "__version__"]
 
 _LOGGER = logging.getLogger(PKG_NAME)
 coloredlogs.install(

bbconf/_version.py

@@ -1 +1 @@
-__version__ = "0.4.2"
+__version__ = "0.5.0"

bbconf/bbagent.py

@@ -0,0 +1,62 @@
+from pathlib import Path
+from typing import Union
+
+from sqlalchemy.orm import Session
+from sqlalchemy.sql import distinct, func, select
+
+from bbconf.config_parser.bedbaseconfig import BedBaseConfig
+from bbconf.db_utils import Bed, BedSets
+from bbconf.models.base_models import StatsReturn
+from bbconf.modules.bedfiles import BedAgentBedFile
+from bbconf.modules.bedsets import BedAgentBedSet
+from bbconf.modules.objects import BBObjects
+
+
+class BedBaseAgent(object):
+    def __init__(
+        self,
+        config: Union[Path, str],
+    ):
+        """
+        Initialize connection to the pep_db database. You can use The basic connection parameters
+        or libpq connection string.
+
+        """
+
+        self.config = BedBaseConfig(config)
+
+        self.__bed = BedAgentBedFile(self.config)
+        self.__bedset = BedAgentBedSet(self.config)
+        self.__objects = BBObjects(self.config)
+
+    @property
+    def bed(self) -> BedAgentBedFile:
+        return self.__bed
+
+    @property
+    def bedset(self) -> BedAgentBedSet:
+        return self.__bedset
+
+    @property
+    def objects(self) -> BBObjects:
+        return self.__objects
+
+    def get_stats(self) -> StatsReturn:
+        """
+        Get statistics for a bed file
+
+        :return: statistics
+        """
+        with Session(self.config.db_engine.engine) as session:
+            number_of_bed = session.execute(select(func.count(Bed.id))).one()[0]
+            number_of_bedset = session.execute(select(func.count(BedSets.id))).one()[0]
+
+            number_of_genomes = session.execute(
+                select(func.count(distinct(Bed.genome_alias)))
+            ).one()[0]
+
+        return StatsReturn(
+            bedfiles_number=number_of_bed,
+            bedsets_number=number_of_bedset,
+            genomes_number=number_of_genomes,
+        )