Creating the SQLAlchemy code for 4 simple tables:

    PhyloplumberGroup - simply holds named groups of users
    PhyloplumberUser - holds the log-in info for a user
    PhyloplumberGroupUser - lists pairs of groups and users to indicate which groups a user belongs to
    ExternalProcess - holds the information about a launched process that is running on the FS

.gitignore

@@ -1,3 +1,4 @@
 *.pyc
 *.db
 phyloplumber.egg-info
+

development.ini

@@ -10,6 +10,10 @@ debug = true
 smtp_server = localhost
 error_email_from = paste@localhost
 
+top_internal_dir = /Users/mholder/Library/Application Support/phyloplumber
+top_external_dir = /Users/mholder/Documents/phyloplumberExternal
+
+
 [server:main]
 use = egg:Paste#http
 host = 127.0.0.1

phyloplumber/lib/__init__.py

@@ -0,0 +1,36 @@
+import os
+from pylons import config
+
+_INTERNAL_DIR = os.path.abspath(os.path.expandvars(os.path.expanduser(config.get('top_internal_dir', '~/internals_phyloplumber'))))
+_EXTERNAL_DIR = os.path.abspath(os.path.expandvars(os.path.expanduser(config.get('top_external_dir', '~/phyloplumber'))))
+
+
+_MISSING_SETTING_MSG = 'A %(setting)s setting is required in the initialization file used to start the server'
+
+def verify_dir(dir):
+    if os.path.exists(dir):
+        if os.path.isdir(dir):
+            return True
+        raise OSError("File %(f)s exists, so a directory cannot be created at that location" % {f : dir})
+    os.makedirs(dir)
+
+def get_top_internal_dir():
+    '''Returns the absolute path to the top directory for "internal" storage.
+    
+    Raises OSError if the directory does not exist and cannot be created.
+    '''
+    if not _INTERNAL_DIR:
+        raise OSError(_MISSING_SETTING_MSG % {'setting' : 'top_internal_dir'})
+    verify_dir(_INTERNAL_DIR)
+    return _INTERNAL_DIR
+
+def get_top_external_dir():
+    '''Returns the absolute path to the top directory for "external" storage.
+    
+    Raises OSError if the directory does not exist and cannot be created.
+    '''
+    if not _EXTERNAL_DIR:
+        raise OSError(_MISSING_SETTING_MSG % {'setting' : 'top_external_dir'})
+    verify_dir(_EXTERNAL_DIR)
+    return _EXTERNAL_DIR
+

phyloplumber/model/__init__.py

@@ -1,7 +1,69 @@
 """The application's model objects"""
-from phyloplumber.model.meta import Session, Base
+import sqlalchemy as sa
+from sqlalchemy import orm, schema
+from sqlalchemy.ext.declarative import declarative_base
+from phyloplumber.model import meta
 
+def now():
+    return datetime.datetime.now()
 
 def init_model(engine):
     """Call me before using any of the tables or classes in the model"""
-    Session.configure(bind=engine)
+    #meta.Session.configure(bind=engine)
+    sm = orm.sessionmaker(autoflush=True, autocommit=False, bind=engine)
+    meta.engine = engine
+    meta.Session = orm.scoped_session(sm)
+    meta.set_metadata(schema.MetaData(bind=engine))
+
+
+    t_group = schema.Table("PhyloplumberGroup", meta.get_metadata(),
+        schema.Column('id', sa.types.Integer,
+            schema.Sequence('groupuser_seq_id', optional=True), primary_key=True),
+        sa.Column("name", sa.types.String, nullable=False),
+        )
+
+    t_user = schema.Table("PhyloplumberUser", meta.metadata,
+        schema.Column('id', sa.types.Integer,
+            schema.Sequence('groupuser_seq_id', optional=True), primary_key=True),
+        sa.Column("username", sa.types.String, nullable=False),
+        sa.Column("fullname", sa.types.String, nullable=False),
+        sa.Column("date_created", sa.types.DateTime, nullable=False),
+        sa.Column("email", sa.types.DateTime, nullable=False),
+        )
+
+    t_process = schema.Table("ExternalProcess", meta.metadata,
+        sa.Column("id", sa.types.String, nullable=False, primary_key=True),
+        sa.Column("parent_dirname", sa.types.String, nullable=False),
+        sa.Column("launch_timestamp", sa.types.DateTime, nullable=False),
+        sa.Column("invocation", sa.types.String, nullable=False),
+        sa.Column("label", sa.types.String, nullable=False),
+        sa.Column("status", sa.types.Integer, nullable=False),
+        sa.Column("service_name", sa.types.String, nullable=False), # this is the controller that launched the job
+        sa.Column("read_group", sa.types.Integer, schema.ForeignKey('PhyloplumberGroup.id')),
+        sa.Column("write_group", sa.types.Integer, schema.ForeignKey('PhyloplumberGroup.id')),
+        )
+
+
+
+    t_group_user = schema.Table('PhyloplumberGroupUser', meta.metadata,
+        schema.Column('id', sa.types.Integer,
+            schema.Sequence('groupuser_seq_id', optional=True), primary_key=True),
+        schema.Column('groupid', sa.types.Integer, schema.ForeignKey('PhyloplumberGroup.id')),
+        schema.Column('userid', sa.types.Integer, schema.ForeignKey('PhyloplumberUser.id')),
+    )
+
+
+    class PhyloplumberGroup(object):
+        pass
+    class PhyloplumberUser(object):
+        pass
+    class PhyloplumberGroupUser(object):
+        pass
+    class ExternalProcess(object):
+        pass
+
+    orm.mapper(PhyloplumberGroup, t_group)
+    orm.mapper(PhyloplumberUser, t_user)
+    orm.mapper(ExternalProcess, t_process)
+    orm.mapper(PhyloplumberGroupUser, t_group_user)
+

phyloplumber/model/meta.py

@@ -1,11 +1,24 @@
 """SQLAlchemy Metadata and Session object"""
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import scoped_session, sessionmaker
+from sqlalchemy import schema
+
 
 __all__ = ['Base', 'Session']
 
 # SQLAlchemy session manager. Updated by model.init_model()
 Session = scoped_session(sessionmaker())
 
-# The declarative Base
-Base = declarative_base()
+metadata = None
+def get_metadata():
+    global metadata
+    return metadata
+def set_metadata(n):
+    global metadata
+    metadata = n
+
+# Assign the same metadata object we created earlier.
+#Base = declarative_base(metadata=metadata)
+
+
+

phyloplumber/websetup.py

@@ -4,7 +4,7 @@
 import pylons.test
 
 from phyloplumber.config.environment import load_environment
-from phyloplumber.model.meta import Session, Base
+from phyloplumber.model.meta import Session, get_metadata
 
 log = logging.getLogger(__name__)
 
@@ -13,6 +13,6 @@ def setup_app(command, conf, vars):
     # Don't reload the app if it was loaded under the testing environment
     if not pylons.test.pylonsapp:
         load_environment(conf.global_conf, conf.local_conf)
-
+    
     # Create the tables if they don't already exist
-    Base.metadata.create_all(bind=Session.bind)
+    get_metadata().create_all(bind=Session.bind)

setup.cfg

@@ -10,7 +10,6 @@ verbose = True
 verbosity = 2
 with-pylons = test.ini
 detailed-errors = 1
-with-doctest = True
 
 # Babel configuration
 [compile_catalog]