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<div style="word-wrap:break-word">Here's one possible solution:
<div>1) make a singleton database handle, as in theDB.py:</div>
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<div>2) use the one handle everywhere it's needed, as in geneticsClasses.py:</div>
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<div>3) also use the handle in the connect() function, in geneticsDBMScommon.py:</div>
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<div>4) query programs then use the dbms entity classes and geneticsDBMScommon, basically like this: </div>
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<div>#!/usr/bin/env python</div>
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<div>from pony.orm import *</div>
<div>import sys, os</div>
<div>import argparse</div>
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</div>
<div>from geneticsDBMScommon import *</div>
<div>from geneticsClasses import *</div>
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</div>
<div>def parseArgs( ):</div>
<div> parser = argparse.ArgumentParser(description="""Analyze variants""" )</div>
<div> parser.add_argument('DBMS', type=str, help="key for the DBMS, an index into the access params in DBMScreds" )</div>
<div> args = parser.parse_args()</div>
<div> return args</div>
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</div>
<div>args=parseArgs()</div>
<div>Connect( args.DBMS, debug=True )</div>
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<div>o o o</div>
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<div>On Nov 5, 2014, at 1:46 PM, Arthur Goldberg <<a href="mailto:Arthur.Goldberg@mssm.edu">Arthur.Goldberg@mssm.edu</a>></div>
<div> wrote:</div>
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<div>On Nov 5, 2014, at 1:29 PM, Arthur Goldberg <<a href="mailto:Arthur.Goldberg@mssm.edu">Arthur.Goldberg@mssm.edu</a>></div>
<div> wrote:</div>
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<div>
<div style="word-wrap:break-word">Hello Alexander
<div><br>
</div>
<div> let me be more specific.</div>
<div> I have a number of modules that query, update, delete against the database.</div>
<div> I want to centralize all the database bind, mapping, and table deletion operations in one module that other modules can call.</div>
<div> Here's my effort to write that centralized module.</div>
<div> The only method is:</div>
<div>Connect( DBMS='arthur_minerva', entityNames=[], dropAndCreateTable=False, debug=False )</div>
<div>DBMS is simply a key into a dictionary of database credential parameters. That works fine, and is used by bind.</div>
<div>entityNames is a list of entities; I want to connect() to make sure that if an entity is declared as a pony db entity then it is in the database</div>
<div>dropAndCreateTable controls whether tables are dropped; if it is true then tables for all entities should be dropped and then created</div>
<div>
<div><br>
</div>
<div> with the call:</div>
<div>
<div>Connect( MyDropAndCreateTables.args.DBMS, entityNames='CNV Subject'.split(), </div>
<div> dropAndCreateTable=True, debug=True )</div>
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<div>
<div> this does not work, however:</div>
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it generates this error:</div>
<div>
<div>b4 db.bind</div>
<div>GET NEW CONNECTION</div>
<div>RELEASE CONNECTION</div>
<div>db.bind</div>
<div>b4 db.generate_mapping</div>
<div>GET CONNECTION FROM THE LOCAL POOL</div>
<div>SET foreign_key_checks = 0</div>
<div>COMMIT</div>
<div>SET foreign_key_checks = 1</div>
<div>CLOSE CONNECTION</div>
<div>db.generate_mapping</div>
<div>entity: CNV</div>
<div>entityObj: <class 'geneticsClasses.CNV'></div>
<div>geneticsDBMScommon.pyc: WARNING: Pony MappingError: Database object is not bound with a provider yet</div>
<div>geneticsDBMScommon.pyc: WARNING: Cannot drop_table()</div>
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<div>I am using mysql. </div>
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<div>On Nov 4, 2014, at 4:39 PM, Alexander Kozlovsky <<a href="mailto:alexander.kozlovsky@gmail.com">alexander.kozlovsky@gmail.com</a>> wrote:</div>
<blockquote type="cite">
<div dir="ltr"><span style="font-family:arial,sans-serif; font-size:13px">Hi Arthur,<br>
<br>
> How can I have the general purpose programs load all the pony entities, but then use only those specified on a command line?<br>
</span><br>
What do you mean by 'use'? Why this general purpose program can't use all entities? Can you provide some example?<br>
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<div class="x_x_gmail_extra"><br>
<div class="x_x_gmail_quote">On Wed, Nov 5, 2014 at 12:24 AM, Goldberg, Arthur P <span dir="ltr">
<<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__mailto-3Aarthur.p.goldberg-40mssm.edu&d=AAMFaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=TntoeYH7lekXzpBRjXwLTkqiWTbWAvp3pHKo_kZp5qI&m=-l9d_YgpS5Br4HVerevDUPDePIdahRQvh6kua6GEKCg&s=8BLVACjagdDyNx90SlAn1F7tsSllEw4K5MHFxb6KM1o&e=" target="_blank">arthur.p.goldberg@mssm.edu</a>></span>
wrote:<br>
<blockquote class="x_x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
Hi Guys<br>
<br>
I've pony entities (class foo(db.Entity), etc.) definitions in multiple modules. And I've several general purpose programs: 1) connect to the dbms and optionally create tables, 2) load a file into a table, etc.<br>
How can I have the general purpose programs load all the pony entities, but then use only those specified on a command line?<br>
<br>
Is this clear?<br>
<br>
thanks<br>
Arthur<br>
<br>
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<div> </div>
<div>Arthur Goldberg
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<div>Seaver Autism Center and Icahn Institute for Genomics & Multiscale Biology</div>
<div>Icahn School of Medicine at Mount Sinai</div>
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<span><geneticsDBMScommon.py></span><span><geneticsSubjects.py></span></blockquote>
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---</div>
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<div>Arthur Goldberg
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