[PonyORM-list] Couple of questions

Alexey Malashkevich alexeymalashkevich at gmail.com
Sun Jun 22 20:57:03 UTC 2014
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Hi Arthur,

There is no need to to change entity names to lower case. According to the
Python naming convention class names should use the CapWords convention:
http://legacy.python.org/dev/peps/pep-0008/#class-names

The lowercase in Python is usually used for naming variables. If you name
your classes using lower case it can decrease readability of your code and
you can mistakenly treat a class name as a variable name or vice versa.

It is normal practice for ORMs when the table name is different from the
entity name. Some mappers use singular names for entities and plural names
for tables by default. Pony doesn't go that far, it just converts the
letter case in accordance with the particular database conventions. You
always can get the table name by reading the _table_ attribute of an entity:

    table_name = Subject._table_

Also, you can specify your table name for an entity during the entity
declaration:

    class Subject(db.Entity):
        _table_ = 'my_table_name'
        ...

Regards,
Alexey



On Sat, Jun 21, 2014 at 11:57 PM, Goldberg, Arthur P <
arthur.p.goldberg at mssm.edu> wrote:

>  Thanks Alexey
>
>  entityName.drop_table(with_all_data=True)
>
>  works. Also, I changed all entity names to lower case, which might avoid
> future problems.
>
>  A
>
>  On Jun 20, 2014, at 7:24 AM, Alexey Malashkevich <
> alexeymalashkevich at gmail.com> wrote:
>
>  This happens because the table name which is generated from the entity
> name is not always equal to the entity name. In MySQL it is recommended to
> convert the names of the tables to the lower case and Pony follows this
> recommendation (see more on this here: http://blog.ponyorm.com/?p=148)
> and due to this the table name for the Subject entity is converted to
> "subject".
>
>  When you call db.drop_table("Subject", if_exists=True) in MySQL on
> Linux, this command cannot find the table "Subject", because the name of
> the table is "subject" and MySQL is case sensitive on Linux.
>
>  In order to delete the table associated with the entity you should use
> the method drop_table of an entity:
>
>      Subject.drop_table(with_all_data=True)
>
>  Another option is to pass the entity class to the method db.drop_table:
>
>     db.drop_table(Subject, with_all_data=True)
>
>  In this case Pony will get the right name of the table.
>
>  Thanks for the question, I've updated the Pony documentation to cover
> this topic http://doc.ponyorm.com/database.html#drop_table
>
>  Regards,
> Alexey
>
>
> On Thu, Jun 19, 2014 at 11:27 PM, Goldberg, Arthur P <
> arthur.p.goldberg at mssm.edu> wrote:
>
>> drop_table() does not work for me. Using MySQL, starting with an empty
>> dbms.
>>
>> #!/usr/bin/env python
>> from pony.orm import *
>> db = Database()
>>
>>  class Variant(db.Entity):
>>     pos = Required(str)
>>     SubjectID = Required("Subject")
>>
>>  class Subject(db.Entity):
>>     FamilyID = Optional(str)
>>     IndivID = PrimaryKey(str)
>>      Sex = Required(str)
>>     variants = Set(Variant)
>>
>>  # dict with params here
>> db.bind('mysql', params["host"], params["user"], params["passwd"],
>> params["db"] )
>>
>>  db.generate_mapping( create_tables=True )
>>
>>  def dropTable( tableName ):
>>     db.drop_table( tableName, if_exists=True, with_all_data=True )
>>
>>  @db_session
>> def inserts():
>>     s1 = Subject(    IndivID = 'sub1',     Sex = '1',)
>>     s2 = Subject(    IndivID = 'sub2',    Sex = '2',)
>>
>>  def main():
>>     inserts()
>>     dropTable('Subject')
>>     inserts()
>>
>>  main()
>>
>>
>>  generates:
>>
>> Traceback (most recent call last):
>>   File
>> "/hpc/users/goldba06/repos/asc_datamanagementandprocessing/dbms_pony/t.py",
>> line 34, in <module>
>>     main()
>>   File
>> "/hpc/users/goldba06/repos/asc_datamanagementandprocessing/dbms_pony/t.py",
>> line 32, in main
>>     inserts()
>>   File "<auto generated wrapper of inserts() function>", line 2, in
>> inserts
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py",
>> line 354, in new_func
>>     finally: self.__exit__(exc_type, exc_value, exc_tb)
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py",
>> line 386, in __exit__
>>     commit()
>>   File "<auto generated wrapper of commit() function>", line 2, in commit
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/utils.py",
>> line 97, in cut_traceback
>>     return func(*args, **kwargs)
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py",
>> line 281, in commit
>>     reraise(CommitException, exceptions)
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py",
>> line 275, in commit
>>     try: primary_cache.commit()
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py",
>> line 941, in commit
>>     if cache.modified: cache.flush()
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py",
>> line 1006, in flush
>>     if obj is not None: obj._save_()
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py",
>> line 3938, in _save_
>>     if status == 'created': obj._save_created_()
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py",
>> line 3838, in _save_created_
>>     % (obj, e.__class__.__name__, msg), e)
>>   File
>> "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/utils.py",
>> line 124, in throw
>>     raise exc
>> pony.orm.core.CommitException: Object Subject['sub1'] cannot be stored in
>> the database. IntegrityError: 1062 Duplicate entry 'sub1' for key 'PRIMARY'
>>
>>
>>  which is what we expect if the table isn't dropped.
>> What I want to do is have these modules:
>> utilities: connect to dbms, and optionally drop a table
>> entities: the entities
>> load file: load a file into a table
>> query: some queries
>> load file, and query optionally use utilities
>>
>>
>>  On Jun 19, 2014, at 10:24 AM, Alexey Malashkevich <
>> alexeymalashkevich at gmail.com> wrote:
>>
>> Hi Arthur,
>>
>>  1. The method which you've used - db.get_connection().executescript()
>> is specific for SQLite only.
>> You need to use the method db.execute() which works for all databases:
>> http://doc.ponyorm.com/database.html#execute
>> Also you can use methods for dropping the database tables:
>> http://doc.ponyorm.com/database.html#drop_table
>> http://doc.ponyorm.com/database.html#drop_all_tables
>>
>>  2. The official way to get all entity attributes is getting the _attrs_
>> attribute from the entity class:
>>
>>      MyEntity._attrs_
>>
>>  It returns the list of all the entity attributes. You can iterate over
>> this list and examine the attribute properties. For example, this is how
>> you can print all attribute names which are not collections (collection
>> means one-to-many relationship attribute):
>>
>>      for attr in MyEntity._attrs_:
>>         if not attr.is_collection:
>>             print attr.name
>>
>>  Below you can see a couple of functions for getting attributes:
>>
>>  def get_all_attrs(entity_cls):
>>     return [ attr for attr in entity_cls._attrs_ ]
>>
>>  def get_attrs_with_columns(entity_cls):
>>     return [ attr for attr in entity_cls._attrs_with_columns_ ]
>>
>>  def get_collection_attrs(entity_cls):
>>     return [ attr for attr in entity_cls._attrs_ if attr.is_collection ]
>>
>>  def get_all_attr_names(entity_cls):
>>     return [ attr.name for attr in entity_cls._attrs_ ]
>>
>>  Please let us know if you have further questions.
>>
>>  Regards,
>> Alexey
>>
>>
>> On Thu, Jun 19, 2014 at 3:13 AM, Goldberg, Arthur P <
>> arthur.p.goldberg at mssm.edu> wrote:
>>
>>> Pony's nifty -- thanks.
>>>
>>>  Some questions:
>>>
>>>  1. Direct SQL. Suppose I want to drop a table. I thought that this
>>> would work because executescript() appears in examples
>>>
>>>         sql = "DROP TABLE IF EXISTS %s;" % tableName
>>>         db.get_connection().executescript(sql)
>>>
>>>
>>>  2. Entity class fields. Suppose I have
>>>
>>>   class Subject(db.Entity):
>>>     FamilyID = Optional(str)
>>>     IndivID = PrimaryKey(str)
>>>     PatID = Optional(str, default='0')
>>>     MatID = Optional(str, default='0')
>>>     Sex = Required(str)
>>>     Pheno = Required(int)
>>>     SampleSet = Required(str)
>>>     variants = Set(Variant)
>>>
>>> className = 'Subject'
>>>
>>> self.slqobj = globals()[ className ]
>>>
>>>   # I can get all fields in Subject with
>>> self.slqobj._attrs_
>>>
>>>
>>>  but is there an official method?
>>>
>>>  Thanks
>>> Arthur
>>>
>>>         ---
>>>
>>> Arthur Goldberg
>>> Associate Professor of Psychiatry
>>> Seaver Autism Center and Icahn Institute for Genomics & Multiscale
>>> Biology
>>> Icahn School of Medicine at Mount Sinai
>>>  Seaver Center, Room ABE-33
>>>  212-241-4229
>>> Arthur.Goldberg at mssm.edu
>>>  Follow us on Twitter @IcahnInstitute
>>> <https://twitter.com/IcahnInstitute>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ponyorm-list mailing list
>>> ponyorm-list at ponyorm.com
>>> /ponyorm-list
>>>
>>>
>>  _______________________________________________
>> ponyorm-list mailing list
>> ponyorm-list at ponyorm.com
>> /ponyorm-list
>>
>>
>>         ---
>>
>> Arthur Goldberg
>> Associate Professor of Psychiatry
>> Seaver Autism Center and Icahn Institute for Genomics & Multiscale Biology
>> Icahn School of Medicine at Mount Sinai
>>  Seaver Center, Room ABE-33
>>  212-241-4229
>> Arthur.Goldberg at mssm.edu
>>  Follow us on Twitter @IcahnInstitute
>> <https://twitter.com/IcahnInstitute>
>>
>>
>>
>>
>>
>> _______________________________________________
>> ponyorm-list mailing list
>> ponyorm-list at ponyorm.com
>> /ponyorm-list
>>
>>
>  _______________________________________________
> ponyorm-list mailing list
> ponyorm-list at ponyorm.com
> /ponyorm-list
>
>
>            ---
>
> Arthur Goldberg
> Associate Professor of Psychiatry
> Seaver Autism Center and Icahn Institute for Genomics & Multiscale Biology
> Icahn School of Medicine at Mount Sinai
>  Seaver Center, Room ABE-33
>  212-241-4229
> Arthur.Goldberg at mssm.edu
>  Follow us on Twitter @IcahnInstitute <https://twitter.com/IcahnInstitute>
>
>
>
>
>
> _______________________________________________
> ponyorm-list mailing list
> ponyorm-list at ponyorm.com
> /ponyorm-list
>
>
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