Separate config

[robinandeer]

Use a function to setup a session explicitly No longer reads a config file

I don't know how to marry this with the automatic version check of the database - if you have any idea about that I'm happy yo listen :)

[ingkebil]

I keep on getting the following error. Is there another connection string I should be using?

Traceback (most recent call last):
  File "/home/kenny.billiau/miniconda/envs/clinstatsdb/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/kenny.billiau/miniconda/envs/clinstatsdb/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/hds/proj/bioinfo/git/kenny/clinstatsdb/clinstatsdb/xparseunaligned.py", line 52, in <module>
    main(sys.argv[1:])
  File "/mnt/hds/proj/bioinfo/git/kenny/clinstatsdb/clinstatsdb/xparseunaligned.py", line 14, in main
    SQL = connect('mysql://tralalala@127.0.0.1:3306/csdb_test')
  File "clinstatsdb/db/store.py", line 10, in connect
    engine = create_engine(connection_string)
  File "/home/kenny.billiau/miniconda/envs/clinstatsdb/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py", line 386, in create_engine
    return strategy.create(*args, **kwargs)
  File "/home/kenny.billiau/miniconda/envs/clinstatsdb/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py", line 75, in create
    dbapi = dialect_cls.dbapi(**dbapi_args)
  File "/home/kenny.billiau/miniconda/envs/clinstatsdb/lib/python2.7/site-packages/sqlalchemy/dialects/mysql/mysqldb.py", line 92, in dbapi
    return __import__('MySQLdb')
ImportError: No module named MySQLdb

[robinandeer]

Probably, I like the pure Python implementation: "pymysql"

I hope you don't mind I made it an explicit dependency over the default MySQL one :)

[ingkebil]

Well, yes, I did remove Python-MySQL and I installed pymysql instead. As is described in the requirements. Ok, the connectionstring becomes mysql+pymysql:// :)

[robinandeer]

Yeah, sorry that ought to do it!

[ingkebil]

Traceback (most recent call last):
  File "/home/kenny.billiau/miniconda/envs/clinstatsdb/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/kenny.billiau/miniconda/envs/clinstatsdb/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/hds/proj/bioinfo/git/kenny/clinstatsdb/clinstatsdb/xparseunaligned.py", line 52, in <module>
    main(sys.argv[1:])
  File "/mnt/hds/proj/bioinfo/git/kenny/clinstatsdb/clinstatsdb/xparseunaligned.py", line 16, in main
    print(Supportparams.exists('/home/clinical/DEMUX//150703_D00134_0206_AH5HGFBCXX/Unaligned4/support.txt')) # 515
  File "clinstatsdb/db/models.py", line 113, in exists
    rs = (cls.query(cls.supportparams_id.label('id'))
TypeError: 'Query' object is not callable

Any idea why class methods calling cls.query don't work anymore?

[ingkebil]

I might have to declare my models in a different way?

[robinandeer]

I didn't test that, sorry. I can have a look but it seems it should still work...

[robinandeer]

it seems like e.g. Project.query already is setup to return Project rows (full)

you could rewrite it as:

project_obj = cls.query.filter_by(projectname=project_name).first()
return project_obj.id if project_obj else False

would that work for you?

[robinandeer]

I mean project_obj will be none if it isn't found in the database so you could return the object or None and handle other stuff downstream maybe?

[ingkebil]

but this will still fall over the fact that cls.query is not callable, no?

db = declarative_base()

class Supportparams(db):
    __tablename__ = 'supportparams'

    supportparams_id = Column(Integer, primary_key=True)
    document_path = Column(String(255), nullable=False)

    @classmethod
    def exists(cls, document_path):
        """Checks if the supportparams entry already exists

        Args:
            document_path (str): Full path to the Unaligned directory

        Returns:
            int: supportparams_id on exists
            False: on not exists

        """
        try:
            rs = (cls.query(cls.supportparams_id.label('id'))
                     .filter(cls.document_path == document_path).one())
            return rs.id
        except NoResultFound:
            return False

[robinandeer]

yeah, I believe cls.query is something like session.query(cls), no? But that's not a problem, is it?

[ingkebil]

According to http://stackoverflow.com/a/14553324/322188 session.query instead of session.query_property should work. And it does :)

[robinandeer]

cool!

[ingkebil]

About the version check of the database: The whole point here was to remove the config file no? So the responsibility to check if this is the latest version of the database now relies on the calling script, not this package. We can remove the Version.latest classmethod and whatever script or package that uses this package will have to check themselves according to their specs/config.

[ingkebil]

haha, so far for me waiting for the :+1: ;)

[robinandeer]

:+1: