Merge pull request #117 from hover2pi/anomoly_db

`jwqldb` interface

docs/source/database.rst

@@ -0,0 +1,7 @@
+********
+database
+********
+
+.. automodule:: jwql.database.database_interface
+    :members:
+    :undoc-members:

docs/source/index.rst

@@ -19,6 +19,7 @@ API documentation
    :maxdepth: 1
    :caption: Contents:
 
+   database.rst
    logging.rst
    monitor_filesystem.rst
    monitor_mast.rst

environment.yml

@@ -14,6 +14,7 @@ dependencies:
 - numpy=1.14.0
 - numpydoc=0.8.0
 - postgresql=9.6.6
+- psycopg2=2.7.5
 - python=3.6.4
 - python-dateutil=2.6.1
 - pytest=3.4.2

jwql/database/database_interface.py

@@ -0,0 +1,158 @@
+"""
+A module to interact with the JWQL postgresql database ``jwqldb``
+
+The ``load_connection()`` function within this module allows the user
+to connect to the ``jwqldb`` database via the ``session``, ``base``,
+and ``engine`` objects (described below).  The classes within serve as
+ORMs (Object-relational mappings) that define the individual tables of
+the relational database.
+
+The ``engine`` object serves as the low-level database API and perhaps
+most importantly contains dialects which allows the ``sqlalchemy``
+module to communicate with the database.
+
+The ``base`` object serves as a base class for class definitions.  It
+produces ``Table`` objects and constructs ORMs.
+
+The ``session`` object manages operations on ORM-mapped objects, as
+construced by the base.  These operations include querying, for
+example.
+
+Authors
+-------
+    Joe Filippazzo, Johannes Sahlmann, Matthew Bourque
+
+"""
+
+from datetime import datetime
+
+import pandas as pd
+from sqlalchemy import Boolean
+from sqlalchemy import Column
+from sqlalchemy import create_engine
+from sqlalchemy import DateTime
+from sqlalchemy import Integer
+from sqlalchemy import MetaData
+from sqlalchemy import String
+from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import sessionmaker
+from sqlalchemy.orm.query import Query
+
+from ..utils import utils
+
+
+SETTINGS = utils.get_config()
+
+
+# Monkey patch Query with data_frame method
+@property
+def data_frame(self):
+    """Method to return a pandas.DataFrame of the results"""
+    return pd.read_sql(self.statement, self.session.bind)
+
+
+Query.data_frame = data_frame
+
+
+def load_connection(connection_string):
+    """Return ``session``, ``base``, ``engine``, and ``metadata``
+    objects for connecting to the ``jwqldb`` database.
+
+    Create an ``engine`` using an given ``connection_string``. Create
+    a ``base`` class and ``session`` class from the ``engine``. Create
+    an instance of the ``session`` class. Return the ``session``,
+    ``base``, and ``engine`` instances. This was stolen from the
+    `ascql` repository.
+
+    Parameters
+    ----------
+    connection_string : str
+        A postgresql database connection string. The
+        connection string should take the form:
+        ``dialect+driver://username:password@host:port/database``
+
+    Returns
+    -------
+    session : sesson object
+        Provides a holding zone for all objects loaded or associated
+        with the database.
+    base : base object
+        Provides a base class for declarative class definitions.
+    engine : engine object
+        Provides a source of database connectivity and behavior.
+    meta: metadata object
+        The connection metadata
+
+    References
+    ----------
+    ``ascql``:
+        https://github.com/spacetelescope/acsql/blob/master/acsql/database/database_interface.py
+    """
+    engine = create_engine(connection_string, echo=False)
+    base = declarative_base(engine)
+    Session = sessionmaker(bind=engine)
+    session = Session()
+    meta = MetaData()
+
+    return session, base, engine, meta
+
+
+session, base, engine, meta = load_connection(SETTINGS['connection_string'])
+
+
+class Anomaly(base):
+    """ORM for the anomalies table"""
+    # Name the table
+    __tablename__ = 'anomalies'
+
+    # Define the columns
+    id = Column(Integer, primary_key=True, nullable=False)
+    filename = Column(String, nullable=False)
+    flag_date = Column(DateTime, nullable=False, default=datetime.now())
+    bowtie = Column(Boolean, nullable=False, default=False)
+    snowball = Column(Boolean, nullable=False, default=False)
+    cosmic_ray_shower = Column(Boolean, nullable=False, default=False)
+    crosstalk = Column(Boolean, nullable=False, default=False)
+    cte_correction_error = Column(Boolean, nullable=False, default=False)
+    data_transfer_error = Column(Boolean, nullable=False, default=False)
+    detector_ghost = Column(Boolean, nullable=False, default=False)
+    diamond = Column(Boolean, nullable=False, default=False)
+    diffraction_spike = Column(Boolean, nullable=False, default=False)
+    dragon_breath = Column(Boolean, nullable=False, default=False)
+    earth_limb = Column(Boolean, nullable=False, default=False)
+    excessive_saturation = Column(Boolean, nullable=False, default=False)
+    figure8_ghost = Column(Boolean, nullable=False, default=False)
+    filter_ghost = Column(Boolean, nullable=False, default=False)
+    fringing = Column(Boolean, nullable=False, default=False)
+    guidestar_failure = Column(Boolean, nullable=False, default=False)
+    banding = Column(Boolean, nullable=False, default=False)
+    persistence = Column(Boolean, nullable=False, default=False)
+    prominent_blobs = Column(Boolean, nullable=False, default=False)
+    trail = Column(Boolean, nullable=False, default=False)
+    scattered_light = Column(Boolean, nullable=False, default=False)
+    other = Column(Boolean, nullable=False, default=False)
+
+    def __repr__(self):
+        """Return the canonical string representation of the object"""
+        # Get the columns that are True
+        a_list = [col for col, val in self.__dict__.items()
+                  if val is True and isinstance(val, bool)]
+
+        txt = ('Anomaly {0.id}: {0.filename} flagged at '
+               '{0.flag_date} for {1}').format(self, a_list)
+
+        return txt
+
+    @property
+    def colnames(self):
+        """A list of all the column names in this table"""
+        # Get the columns
+        a_list = [col for col, val in self.__dict__.items()
+                  if isinstance(val, bool)]
+
+        return a_list
+
+
+if __name__ == '__main__':
+
+    base.metadata.create_all(engine)