Migrate schema to match Bioconductor's BiocFileCache. (#12)

- Mostly changing some of the fields from varchar to text (#11)
- Update contributor list
- Update Changelog

Co-authored-by: Khoroshevskyi <[email protected]>

AUTHORS.md

@@ -2,3 +2,4 @@
 
 * Jayaram Kancherla <[email protected]>
 * Max Hargreaves <[email protected]>
+* Oleksandr Khoroshevskyi <[email protected]>

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
-## Version 0.1 (development)
+## Version 0.4 (development)
 
-- Initial release
+- Migrate the schema to match R/Bioconductor's BiocFileCache (Check out [this issue](https://github.com/BiocPy/pyBiocFileCache/issues/11)). Thanks to [@khoroshevskyi ](https://github.com/khoroshevskyi) for the PR.
+
+## Version 0.1 
+
+- Initial release of the package, Setting up all the actions.

docs/conf.py

@@ -179,10 +179,7 @@ def setup(app):
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-html_theme_options = {
-    "sidebar_width": "300px",
-    "page_width": "1200px"
-}
+html_theme_options = {"sidebar_width": "300px", "page_width": "1200px"}
 
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []
@@ -266,9 +263,7 @@ def setup(app):
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
-    ("index", "user_guide.tex", "pyBiocFileCache Documentation", "jkanche", "manual")
-]
+latex_documents = [("index", "user_guide.tex", "pyBiocFileCache Documentation", "jkanche", "manual")]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
@@ -304,4 +299,4 @@ def setup(app):
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }
 
-print(f"loading configurations for {project} {version} ...", file=sys.stderr)
+print(f"loading configurations for {project} {version} ...", file=sys.stderr)

src/pybiocfilecache/BiocFileCache.py

@@ -9,8 +9,7 @@
 from sqlalchemy.orm import Session
 
 from ._exceptions import NoFpathError, RnameExistsError, RpathTimeoutError
-from .db import create_schema
-from .db.schema import Resource
+from .db.db_config import create_schema, Resource
 from .utils import copy_or_move, create_tmp_dir, generate_id
 
 __author__ = "Jayaram Kancherla"

src/pybiocfilecache/__init__.py

@@ -17,8 +17,8 @@
 
 from .BiocFileCache import BiocFileCache as BiocFileCache
 
-from .db.schema import Metadata as Metadata
-from .db.schema import Resource as Resource
+from .db.db_config import Metadata as Metadata
+from .db.db_config import Resource as Resource
 
 from ._exceptions import NoFpathError as NoFpathError
 from ._exceptions import RnameExistsError as RnameExistsError

src/pybiocfilecache/const.py

@@ -0,0 +1 @@
+SCHEMA_VERSION = "0.99.4"

src/pybiocfilecache/db/__init__.py

@@ -2,4 +2,4 @@
 __copyright__ = "jkanche"
 __license__ = "MIT"
 
-from .Base import create_schema
+from .db_config import create_schema

src/pybiocfilecache/db/db_config.py

@@ -0,0 +1,84 @@
+from typing import Tuple
+
+from sqlalchemy import create_engine, select, Column, Integer, Text, DateTime, func
+from sqlalchemy.engine import Engine
+from sqlalchemy.orm.session import Session
+
+from sqlalchemy.orm import declarative_base, sessionmaker
+
+from ..const import SCHEMA_VERSION
+
+__author__ = "jkanche"
+__copyright__ = "jkanche"
+__license__ = "MIT"
+
+Base = declarative_base()
+
+
+class Metadata(Base):
+    __tablename__ = "metadata"
+    key = Column(Text(), primary_key=True, index=True)
+    value = Column(Text())
+
+    def __repr__(self):
+        return "<Metadata(key='%s', valye='%s')>" % (self.key, self.value)
+
+
+class Resource(Base):
+    __tablename__ = "resource"
+    id = Column(Integer, primary_key=True, index=True, autoincrement=True)
+    rid = Column(Text())
+    rname = Column(Text())
+    create_time = Column(DateTime, server_default=func.now())
+    access_time = Column(DateTime, server_default=func.now())
+    rpath = Column(Text())
+    rtype = Column(Text())
+    fpath = Column(Text())
+    last_modified_time = Column(DateTime, onupdate=func.now())
+    etag = Column(Text())
+    expires = Column(DateTime)
+
+    def __repr__(self):
+        return "<Resource(id='%s', rname='%s')>" % (self.id, self.rname)
+
+
+def add_metadata(key: str, value: str, engine: Engine) -> None:
+    """Add metadata to the database.
+
+    Args:
+        key:
+            Key of the metadata.
+        value:
+            Value of the metadata.
+        engine:
+            Engine
+    """
+    with Session(engine) as session:
+        if session.scalar(select(Metadata).where(Metadata.key == key)):
+            pass
+        else:
+            new_metadata = Metadata(key=key, value=value)
+            session.add(new_metadata)
+            session.commit()
+
+
+def create_schema(cache_dir: str) -> Tuple[Engine, sessionmaker]:
+    """Create the schema in the sqlite database.
+
+    Args:
+        cache_dir:
+            Location where the cache directory.
+
+    Returns:
+        A tuple of sqlalchemy engine and session maker.
+    """
+    engine = create_engine(
+        f"sqlite:///{cache_dir}", connect_args={"check_same_thread": False}
+    )
+
+    Base.metadata.create_all(bind=engine, checkfirst=True)
+    sessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
+
+    add_metadata("schema_version", SCHEMA_VERSION, engine)
+
+    return (engine, sessionLocal)

tests/conftest.py

@@ -1,9 +1,8 @@
 """Dummy conftest.py for pybiocfilecache.
-
 If you don't know what this is for, just leave it empty.
 Read more about conftest.py under:
 - https://docs.pytest.org/en/stable/fixture.html
 - https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
-# import pytest
+# import pytest