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Also, I am unalbe to drop a table with execute():
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<div>params = { 'host':'db', 'user':'', 'passwd':'', 'db':''} # data removed</div>
<div><br>
</div>
<div>from pony.orm import *</div>
<div>from geneticsClasses import db</div>
<div><br>
</div>
<div>@db_session</div>
<div>def dropTable( tableName ):</div>
<div> sql = """SET foreign_key_checks = 0; DROP TABLE IF EXISTS """ + tableName + """; SET foreign_key_checks = 1;"""</div>
<div> db.execute( sql )</div>
<div> print 'dropped ', tableName</div>
<div><br>
</div>
<div>def Connect( tableName, dropAndCreateTable=False ):</div>
<div> db.bind('mysql', params["host"], params["user"], params["passwd"], params["db"] )</div>
<div><br>
</div>
<div> db.generate_mapping( create_tables=dropAndCreateTable )</div>
<div><br>
</div>
<div> if dropAndCreateTable:</div>
<div> dropTable( tableName )</div>
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<div>generates:</div>
</div>
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<blockquote type="cite">
<div>Exception _mysql_exceptions.ProgrammingError: (2014, "Commands out of sync; you can't run this command now") in <bound method Cursor.__del__ of <MySQLdb.cursors.Cursor object at 0x1acab50>> ignored</div>
<div>Traceback (most recent call last):</div>
<div> File "/hpc/users/goldba06/repos/asc_datamanagementandprocessing/dbms_pony/insertFileIntoTable.py", line 150, in <module></div>
<div>SET foreign_key_checks = 0; DROP TABLE IF EXISTS Subject; SET foreign_key_checks = 1;</div>
<div>dropped Subject</div>
<div> Connect( MyLoadFile.args.className, dropAndCreateTable=MyLoadFile.args.dropAndCreateTable )</div>
<div> File "/hpc/users/goldba06/repos/asc_datamanagementandprocessing/dbms_pony/geneticsDBMScommon.py", line 31, in Connect</div>
<div> dropTable( tableName )</div>
<div> File "<auto generated wrapper of dropTable() function>", line 2, in dropTable</div>
<div> File "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py", line 354, in new_func</div>
<div> finally: self.__exit__(exc_type, exc_value, exc_tb)</div>
<div> File "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py", line 386, in __exit__</div>
<div> commit()</div>
<div> File "<auto generated wrapper of commit() function>", line 2, in commit</div>
<div> File "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/utils.py", line 97, in cut_traceback</div>
<div> return func(*args, **kwargs)</div>
<div> File "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py", line 281, in commit</div>
<div> reraise(CommitException, exceptions)</div>
<div> File "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py", line 275, in commit</div>
<div> try: primary_cache.commit()</div>
<div> File "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py", line 949, in commit</div>
<div> cache.rollback()</div>
<div> File "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/core.py", line 960, in rollback</div>
<div> try: provider.rollback(connection)</div>
<div> File "<auto generated wrapper of rollback() function>", line 2, in rollback</div>
<div> File "/hpc/users/goldba06/.local/lib/python2.7/site-packages/pony/orm/dbapiprovider.py", line 45, in wrap_dbapi_exceptions</div>
<div> except dbapi_module.ProgrammingError, e: raise ProgrammingError(e)</div>
<div>pony.orm.core.CommitException: ProgrammingError: 2014 Commands out of sync; you can't run this command now</div>
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<div>On Jun 19, 2014, at 10:24 AM, Alexey Malashkevich <<a href="mailto:alexeymalashkevich@gmail.com">alexeymalashkevich@gmail.com</a>> wrote:</div>
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<blockquote type="cite">
<div dir="ltr">Hi Arthur,
<div><br>
</div>
<div>1. The method which you've used - db.get_connection().executescript() is specific for SQLite only. </div>
<div>You need to use the method db.execute() which works for all databases: <a href="http://doc.ponyorm.com/database.html#execute" target="_blank">
http://doc.ponyorm.com/database.html#execute</a></div>
<div>Also you can use methods for dropping the database tables:</div>
<div><a href="http://doc.ponyorm.com/database.html#drop_table" target="_blank">http://doc.ponyorm.com/database.html#drop_table</a></div>
<div><a href="http://doc.ponyorm.com/database.html#drop_all_tables" target="_blank">http://doc.ponyorm.com/database.html#drop_all_tables</a></div>
<div><br>
</div>
<div>2. The official way to get all entity attributes is getting the _attrs_ attribute from the entity class:</div>
<div><br>
</div>
<div> MyEntity._attrs_</div>
<div><br>
</div>
<div>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):</div>
<div><br>
</div>
<div> for attr in MyEntity._attrs_:</div>
<div> if not <a href="http://attr.is">attr.is</a>_collection:</div>
<div> print <a href="http://attr.name/" target="_blank">attr.name</a></div>
<div><br>
</div>
<div>Below you can see a couple of functions for getting attributes:</div>
<div>
<div><br>
</div>
<div>def get_all_attrs(entity_cls):</div>
<div> return [ attr for attr in entity_cls._attrs_ ]</div>
<div><br>
</div>
<div>def get_attrs_with_columns(entity_cls):</div>
<div> return [ attr for attr in entity_cls._attrs_with_columns_ ]</div>
<div><br>
</div>
<div>def get_collection_attrs(entity_cls):</div>
<div> return [ attr for attr in entity_cls._attrs_ if <a href="http://attr.is">
attr.is</a>_collection ]</div>
<div><br>
</div>
<div>def get_all_attr_names(entity_cls):</div>
<div> return [ <a href="http://attr.name/">attr.name</a> for attr in entity_cls._attrs_ ]</div>
</div>
<div><br>
</div>
<div>Please let us know if you have further questions.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Alexey</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Thu, Jun 19, 2014 at 3:13 AM, Goldberg, Arthur P <span dir="ltr">
<<a>arthur.p.goldberg@mssm.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Pony's nifty -- thanks.
<div><br>
</div>
<div>Some questions:</div>
<div><br>
</div>
<div>1. Direct SQL. Suppose I want to drop a table. I thought that this would work because executescript() appears in examples</div>
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<blockquote type="cite">
<div> sql = "DROP TABLE IF EXISTS %s;" % tableName</div>
<div> db.get_connection().executescript(sql)</div>
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<div><br>
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</div>
<div>2. Entity class fields. Suppose I have</div>
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<div>class Subject(db.Entity):</div>
<div> FamilyID = Optional(str)</div>
<div> IndivID = PrimaryKey(str)</div>
<div> PatID = Optional(str, default='0')</div>
<div> MatID = Optional(str, default='0')</div>
<div> Sex = Required(str)</div>
<div> Pheno = Required(int)</div>
<div> SampleSet = Required(str)</div>
<div> variants = Set(Variant)</div>
</blockquote>
<blockquote type="cite">className = 'Subject' </blockquote>
<blockquote type="cite">self.slqobj = globals()[ className ]</blockquote>
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<blockquote type="cite">
<div># I can get all fields in Subject with</div>
<div>self.slqobj._attrs_</div>
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<div><br>
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<div>but is there an official method?</div>
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<div>Thanks</div>
<div>Arthur</div>
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---</div>
<div> </div>
<div>Arthur Goldberg
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---</div>
<div> </div>
<div>Arthur Goldberg
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