pyiron_base.database.generic module

DatabaseAccess class deals with accessing the database

class pyiron_base.database.generic.AutorestoredConnection(engine, timeout=60)

Bases: object

close()

commit()

execute(*args, **kwargs)

execute_once(*args, **kwargs)

class pyiron_base.database.generic.ConnectionWatchDog(conn, lock, timeout=60)

Bases: Thread

Helper class that closes idle connections after a given timeout.

Initialize it with the connection to watch and a lock that protects it. The lock prevents the watchdog from killing a connection that is currently used. The timeout is in seconds.

>>> conn = SqlConnection(...)
>>> lock = threading.Lock()
>>> dog = ConnectionWatchDog(conn, lock, timeout=60)

After it is created, :method:`.kick()` the watchdog periodically before the timeout runs out. It is important to acquire the lock when using the connection object.

>>> dog.kick()
>>> with lock:
...    conn.execute(...)
>>> dog.kick()

Once you want to finish the connection or want to make sure the watchdog quit, call :method:`.kill()` to shut it down. This also causes the watch dog to try and close the connection.

>>> dog.kill()

kick()

Restarts the timeout.

kill()

Stop the watchdog and close the connection.

run()

Starts the watchdog.

class pyiron_base.database.generic.DatabaseAccess(connection_string, table_name, timeout=60)

Bases: IsDatabase

A core element of PyIron, which generally deals with accessing the database: getting, sending, changing some data to the db.

Parameters:

• connection_string (str) – SQLalchemy connection string which specifies the database to connect to typical form: dialect+driver://username:password@host:port/database example: ‘postgresql://scott:tiger@cmcent56.mpie.de/mdb’

• table_name (str) – database table name, a simple string like: ‘simulation’

Murat Han Celik

add_column(col_name, col_type)

Add an additional column - required for modification on the database

Parameters:

• col_name (str, list) – name of the new column, normal string like: ‘myColumn’

• (str (col_type) – SQL type of the new column, SQL type like: ‘varchar(50)’

• list – SQL type of the new column, SQL type like: ‘varchar(50)’

Returns:

add_item_dict(par_dict)

Create a new database item

Parameters:

par_dict (dict) –

Dictionary with the item values and column names as keys, like:

{‘chemicalformula’: ‘BO’,

’computer’: ‘localhost’, ‘hamilton’: ‘VAMPS’, ‘hamversion’: ‘1.1’, ‘job’: ‘testing’, ‘subjob’ : ‘SubJob’, ‘parentid’: 0L, ‘myCol’: ‘Blubbablub’, ‘project’: ‘database.testing’, ‘projectpath’: ‘/root/directory/tmp’, ‘status’: ‘KAAAA’, ‘timestart’: datetime(2016, 5, 2, 11, 31, 4, 253377), ‘timestop’: datetime(2016, 5, 2, 11, 31, 4, 371165), ‘totalcputime’: 0.117788, ‘username’: ‘Test’}

Returns:

Database ID of the item created as an int, like: 3

Return type:

int

change_column_type(col_name, col_type)

Modify data type of an existing column - required for modification on the database

Parameters:

• col_name (str, list) – name of the new column, normal string like: ‘myColumn’

• (str (col_type) – SQL type of the new column, SQL type like: ‘varchar(50)’

• list – SQL type of the new column, SQL type like: ‘varchar(50)’

Returns:

delete_item(item_id: int)

Delete Item from database

Parameters:

item_id (int) – Databse Item ID (Integer), like: 38

Returns:

get_item_by_id(item_id)

Get item from database by searching for a specific item Id.

Parameters:

item_id (int) – Databse Item ID (Integer), like: 38

Returns:

Dictionary where the key is the column name, like:

{‘chemicalformula’: u’BO’,

’computer’: u’localhost’, ‘hamilton’: u’VAMPS’, ‘hamversion’: u’1.1’, ‘id’: 1, ‘job’: u’testing’, ‘masterid’: None, ‘parentid’: 0, ‘project’: u’database.testing’, ‘projectpath’: u’/root/directory/tmp’, ‘status’: u’KAAAA’, ‘subjob’: u’SubJob’, ‘timestart’: datetime.datetime(2016, 5, 2, 11, 31, 4, 253377), ‘timestop’: datetime.datetime(2016, 5, 2, 11, 31, 4, 371165), ‘totalcputime’: 0.117788, ‘username’: u’Test’}

Return type:

dict

get_items_dict(item_dict, return_all_columns=True)

Parameters:

• item_dict (dict) –

  a dict type, which has a certain syntax for this function: a normal dict like {‘hamilton’: ‘VAMPE’, ‘hamversion’: ‘1.1’} has similarities with a simple query like

  select * from table_name where hamilton = ‘VAMPE AND hamversion = ‘1.1’

  as seen it puts an AND for every key, value combination in the dict and searches for it.

  another syntax is for an OR statement, simply: {‘hamilton’: [‘VAMPE’, ‘LAMMPS’]}, the query would be:

  select * from table_name where hamilton = ‘VAMPE’ OR hamilton = ‘LAMMPS’

  and lastly for a LIKE statement, simply: {‘project’: ‘database.%’}, the query would be

  select * from table_name where project LIKE ‘database.%’

  that means you can simply add the syntax for a like statement like ‘%’ and it will automatically operate a like-search

  of course you can also use a more complex select method, with everything in use:

  {‘hamilton’: [‘VAMPE’, ‘LAMMPS’],

  ’project’: ‘databse%’, ‘hamversion’: ‘1.1’}

  select * from table_name where (hamilton = ‘VAMPE’ Or hamilton = ‘LAMMPS’) AND

  (project LIKE ‘database%’) AND hamversion = ‘1.1’

• return_all_columns (bool) – return all columns or only the ‘id’ - still the format stays the same.

Returns:

the function returns a list of dicts like get_items_sql, but it does not format datetime:

[{‘chemicalformula’: u’Ni108’,

’computer’: u’mapc157’, ‘hamilton’: u’LAMMPS’, ‘hamversion’: u’1.1’, ‘id’: 24, ‘job’: u’DOF_1_0’, ‘parentid’: 21L, ‘project’: u’lammps.phonons.Ni_fcc’, ‘projectpath’: u’D:/PyIron/PyIron_data/projects’, ‘status’: u’finished’, ‘timestart’: datetime.datetime(2016, 6, 24, 10, 17, 3, 140000), ‘timestop’: datetime.datetime(2016, 6, 24, 10, 17, 3, 173000), ‘totalcputime’: 0.033, ‘username’: u’test’},

{‘chemicalformula’: u’Ni108’,

’computer’: u’mapc157’, ‘hamilton’: u’LAMMPS’, ‘hamversion’: u’1.1’, ‘id’: 21, ‘job’: u’ref’, ‘parentid’: 20L, ‘project’: u’lammps.phonons.Ni_fcc’, ‘projectpath’: u’D:/PyIron/PyIron_data/projects’, ‘status’: u’finished’, ‘timestart’: datetime.datetime(2016, 6, 24, 10, 17, 2, 429000), ‘timestop’: datetime.datetime(2016, 6, 24, 10, 17, 2, 463000), ‘totalcputime’: 0.034, ‘username’: u’test’},…….]

Return type:

list

get_items_sql(where_condition=None, sql_statement=None)

Submit an SQL query to the database

Parameters:

• where_condition (str) – SQL where query, query like: “project LIKE ‘lammps.phonons.Ni_fcc%’”

• sql_statement (str) – general SQL query, normal SQL statement

Returns:

get a list of dictionaries, where each dictionary represents one item of the table like:

[{u’chemicalformula’: u’BO’,

u’computer’: u’localhost’, u’hamilton’: u’VAMPS’, u’hamversion’: u’1.1’, u’id’: 1, u’job’: u’testing’, u’masterid’: None, u’parentid’: 0, u’project’: u’database.testing’, u’projectpath’: u’/TESTING’, u’status’: u’KAAAA’, u’subjob’: u’testJob’, u’timestart’: u’2016-05-02 11:31:04.253377’, u’timestop’: u’2016-05-02 11:31:04.371165’, u’totalcputime’: 0.117788, u’username’: u’User’},

{u’chemicalformula’: u’BO’,

u’computer’: u’localhost’, u’hamilton’: u’VAMPS’, u’hamversion’: u’1.1’, u’id’: 2, u’job’: u’testing’, u’masterid’: 0, u’parentid’: 0, u’project’: u’database.testing’, u’projectpath’: u’/TESTING’, u’status’: u’KAAAA’, u’subjob’: u’testJob’, u’timestart’: u’2016-05-02 11:31:04.253377’, u’timestop’: u’2016-05-02 11:31:04.371165’, u’totalcputime’: 0.117788, u’username’: u’User’}…..]

Return type:

list

get_job_status(job_id)

get_job_working_directory(job_id)

query_for_element(element)

static regexp(expr, item)

Regex function for SQLite :param expr: str, regex expression :param item: str, item which needs to be checked

Returns:

property view_mode

Get view_mode - if view_moded is enable pyiron has read only access to the database.

Some implementations do not allow to set this value.

Returns:

True when view_mode is enabled

Return type:

bool

property viewer_mode

Get view_mode - if view_moded is enable pyiron has read only access to the database.

Some implementations do not allow to set this value.

Returns:

True when view_mode is enabled

Return type:

bool