Merge pull request #114 from pepkit/dev

Release v0.7.0

.github/workflows/python-publish.yml

@@ -1,6 +1,3 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: Upload Python Package
 
 on:
@@ -9,9 +6,10 @@ on:
 
 jobs:
   deploy:
-
+    name: upload release to PyPI
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
@@ -23,9 +21,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
     - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel
-        twine upload dist/*
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

docs/README.md

@@ -45,12 +45,12 @@ agent.project.create(prj_obj, namespace, name, tag)
 # examples of update_dict:
 update_dict1 = {"is_private" = True}
 update_dict2 = {"is_private" = True, name = "new_name"}
-update_dict3 = {"project" = prj_obj, "is_private"=True}
+update_dict3 = {"project" = prj_obj, "is_private" = True}
 update_dict4 = {"project" = prj_obj}
 update_dict4 = {"tag" = "new_tag"}
 
 # after creation of the dict, update record by providing update_dict and namespace, name and tag:
-agent.project.update(update_dict, namespace, name, tag)
+agent.project.update(update_dict, namespace, name, tag, )
 
 # retrieve a project
 agent.project.get(namespace, name, tag)

docs/changelog.md

@@ -2,6 +2,15 @@
 
 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.
 
+## [0.7.0] -- 2023-01-17
+- Added `pop` to project table and annotation model [#107](https://github.com/pepkit/pepdbagent/issues/107)
+- Added `forked_from` feature [#73](https://github.com/pepkit/pepdbagent/issues/73)
+- Switched to pydantic2 [#105](https://github.com/pepkit/pepdbagent/issues/105)
+- Updated requirements (psycopg2 -> psycopg3) [#102](https://github.com/pepkit/pepdbagent/issues/102)
+- Added sample module that contains functionality for updating, adding, and deleting samples in the project separately [#111](https://github.com/pepkit/pepdbagent/issues/111)
+- Added user and favorite tables with functionality [#104](https://github.com/pepkit/pepdbagent/issues/104)
+- Updated the sample update method when updating the whole project. Following this change, samples are updated without changing the ID in the database
+
 ## [0.6.0] -- 2023-08-24
 - Added date filter to project annotation
 

pepdbagent/__init__.py

@@ -2,8 +2,11 @@
 import coloredlogs
 import logmuse
 
-from ._version import __version__
-from .pepdbagent import *
+from pepdbagent._version import __version__
+from pepdbagent.pepdbagent import PEPDatabaseAgent
+
+__all__ = ["__version__", "PEPDatabaseAgent"]
+
 
 _LOGGER = logmuse.init_logger("pepdbagent")
 coloredlogs.install(

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.6.0"
+__version__ = "0.7.0"

pepdbagent/const.py

@@ -12,7 +12,7 @@
 DEFAULT_LIMIT = 100
 
 # db_dialects
-POSTGRES_DIALECT = "postgresql"
+POSTGRES_DIALECT = "postgresql+psycopg"
 
 DEFAULT_LIMIT_INFO = 5
 

pepdbagent/db_utils.py

@@ -1,19 +1,17 @@
 import datetime
 import logging
-from typing import Any, Optional, List
+from typing import Optional, List
 
 from sqlalchemy import (
     BigInteger,
     FetchedValue,
-    PrimaryKeyConstraint,
     Result,
     Select,
     String,
     event,
     select,
     TIMESTAMP,
     ForeignKey,
-    ForeignKeyConstraint,
     UniqueConstraint,
 )
 from sqlalchemy.dialects.postgresql import JSON
@@ -87,17 +85,41 @@ class Projects(Base):
     config: Mapped[dict] = mapped_column(JSON, server_default=FetchedValue())
     private: Mapped[bool]
     number_of_samples: Mapped[int]
+    number_of_stars: Mapped[int] = mapped_column(default=0)
     submission_date: Mapped[datetime.datetime]
     last_update_date: Mapped[Optional[datetime.datetime]] = mapped_column(
         onupdate=deliver_update_date, default=deliver_update_date
     )
     pep_schema: Mapped[Optional[str]]
+    pop: Mapped[Optional[bool]] = mapped_column(default=False)
     samples_mapping: Mapped[List["Samples"]] = relationship(
         back_populates="sample_mapping", cascade="all, delete-orphan"
     )
     subsamples_mapping: Mapped[List["Subsamples"]] = relationship(
         back_populates="subsample_mapping", cascade="all, delete-orphan"
     )
+    stars_mapping: Mapped[List["Stars"]] = relationship(
+        back_populates="project_mapping", cascade="all, delete-orphan"
+    )
+    views_mapping: Mapped[List["Views"]] = relationship(
+        back_populates="project_mapping", cascade="all, delete-orphan"
+    )
+
+    # Self-referential relationship. The parent project is the one that was forked to create this one.
+    forked_from_id: Mapped[Optional[int]] = mapped_column(
+        ForeignKey("projects.id", ondelete="SET NULL"), nullable=True
+    )
+    forked_from_mapping = relationship(
+        "Projects",
+        back_populates="forked_to_mapping",
+        remote_side=[id],
+        single_parent=True,
+        cascade="all",
+    )
+
+    forked_to_mapping = relationship(
+        "Projects", back_populates="forked_from_mapping", cascade="all"
+    )
 
     __table_args__ = (UniqueConstraint("namespace", "name", "tag"),)
 
@@ -113,8 +135,13 @@ class Samples(Base):
     sample: Mapped[dict] = mapped_column(JSON, server_default=FetchedValue())
     row_number: Mapped[int]
     project_id = mapped_column(ForeignKey("projects.id", ondelete="CASCADE"))
+    sample_name: Mapped[Optional[str]] = mapped_column()
     sample_mapping: Mapped["Projects"] = relationship(back_populates="samples_mapping")
 
+    views: Mapped[Optional[List["ViewSampleAssociation"]]] = relationship(
+        back_populates="sample", cascade="all, delete-orphan"
+    )
+
 
 class Subsamples(Base):
     """
@@ -131,6 +158,67 @@ class Subsamples(Base):
     subsample_mapping: Mapped["Projects"] = relationship(back_populates="subsamples_mapping")
 
 
+class User(Base):
+    """
+    User table representation in the database
+    """
+
+    __tablename__ = "users"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    namespace: Mapped[str]
+    stars_mapping: Mapped[List["Stars"]] = relationship(
+        back_populates="user_mapping", cascade="all, delete-orphan"
+    )
+
+
+class Stars(Base):
+    """
+    FavoriteProjects table representation in the database
+    """
+
+    __tablename__ = "stars"
+
+    user_id = mapped_column(ForeignKey("users.id", ondelete="CASCADE"), primary_key=True)
+    project_id = mapped_column(ForeignKey("projects.id", ondelete="CASCADE"), primary_key=True)
+    user_mapping: Mapped[List["User"]] = relationship(back_populates="stars_mapping")
+    project_mapping: Mapped["Projects"] = relationship(back_populates="stars_mapping")
+
+
+class Views(Base):
+    """
+    Views table representation in the database
+    """
+
+    __tablename__ = "views"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    name: Mapped[str] = mapped_column()
+    description: Mapped[Optional[str]]
+
+    project_id = mapped_column(ForeignKey("projects.id", ondelete="CASCADE"))
+    project_mapping = relationship("Projects", back_populates="views_mapping")
+
+    samples: Mapped[List["ViewSampleAssociation"]] = relationship(
+        back_populates="view", cascade="all, delete-orphan"
+    )
+
+    _table_args__ = (UniqueConstraint("namespace", "project_id"),)
+
+
+class ViewSampleAssociation(Base):
+    """
+    Association table between views and samples
+    """
+
+    __tablename__ = "views_samples"
+
+    sample_id = mapped_column(ForeignKey("samples.id", ondelete="CASCADE"), primary_key=True)
+    view_id = mapped_column(ForeignKey("views.id", ondelete="CASCADE"), primary_key=True)
+    sample: Mapped["Samples"] = relationship(back_populates="views")
+    view: Mapped["Views"] = relationship(back_populates="samples")
+
+
 class BaseEngine:
     """
     A class with base methods, that are used in several classes. e.g. fetch_one or fetch_all

pepdbagent/exceptions.py

@@ -36,3 +36,40 @@ def __init__(self, msg=""):
 class FilterError(PEPDatabaseAgentError):
     def __init__(self, msg=""):
         super().__init__(f"""pepdbagent filter error. {msg}""")
+
+
+class ProjectNotInFavorites(PEPDatabaseAgentError):
+    """
+    Project doesn't exist in favorites
+    """
+
+    def __init__(self, msg=""):
+        super().__init__(f"""Project is not in favorites list. {msg}""")
+
+
+class ProjectAlreadyInFavorites(PEPDatabaseAgentError):
+    """
+    Project doesn't exist in favorites
+    """
+
+    def __init__(self, msg=""):
+        super().__init__(f"""Project is already in favorites list. {msg}""")
+
+
+class SampleNotFoundError(PEPDatabaseAgentError):
+    def __init__(self, msg=""):
+        super().__init__(f"""Sample does not exist. {msg}""")
+
+
+class ViewNotFoundError(PEPDatabaseAgentError):
+    def __init__(self, msg=""):
+        super().__init__(f"""View does not exist. {msg}""")
+
+
+class SampleAlreadyInView(PEPDatabaseAgentError):
+    """
+    Sample is already in the view exception
+    """
+
+    def __init__(self, msg=""):
+        super().__init__(f"""Sample is already in the view. {msg}""")