Creating a new schema name during migration with Alembic

[Josie Barth]

Hello,

I'm building an application using Flask as the web framework, PostgreSQL 
for the database, and Flask-SQLAlchemy to communicate between the two (I'm 
still very new to all these technologies.)  I want to use Alembic to 
migrate my SQLAlchemy tables that I've created in a models.py file to 
PostgreSQL.  I'm using the code from the "Local Migration" section 
specified in the following tutorial:

https://realpython.com/blog/python/flask-by-example-part-2-postgres-sqlalchemy-and-alembic/


Here is an example of one my tables, where I've attached it to an explicit 
schema: 
___ 

class Student(db.Model):
__tablename__ = 'Students'
# __table_args__ = {u'schema': 'OurHouse'}

Id = db.Column(db.Integer, primary_key=True, 
server_default=db.FetchedValue())
FirstName = db.Column(db.String(50), nullable=False)
LastName = db.Column(db.String(50), nullable=False)
Email = db.Column(db.String(62), nullable=False)
Phone = db.Column(db.String(10), nullable=False)
IsActive = db.Column(db.Boolean, nullable=False)
CreatedAt = db.Column(db.DateTime(True), nullable=False)
UpdatedAt = db.Column(db.DateTime(True), nullable=False)

___

I have no problems doing the first two steps (initializing Alembic and 
creating the migration):

$ python manage.py db init 

$ python manage.py db migrate


I do have an issue when I attempt to run:

$ python manage.py db upgrade

Basically, I get the error that "OurHouse" isn't a schema, and I don't know 
how to go about creating one in the migration file that is generated.  I'm 
thinking I need to do something like this:

"""empty message

Revision ID: c6a019bc79e1
Revises: 
Create Date: 2017-03-01 21:55:02.360888

"""
from alembic import op
import sqlalchemy as sa


# revision identifiers, used by Alembic.
revision = 'c6a019bc79e1'
down_revision = None
branch_labels = None
depends_on = None

def upgrade():

  # Not sure if this is possible:

op.create_schema('OurHouse')


 # This is what's given, along with the code for my other tables: 

op.create_table('Students',
sa.Column('Id', sa.Integer(), server_default=sa.FetchedValue(), 
nullable=False),
sa.Column('FirstName', sa.String(length=50), nullable=False),
sa.Column('LastName', sa.String(length=50), nullable=False),
sa.Column('Email', sa.String(length=62), nullable=False),
sa.Column('Phone', sa.String(length=10), nullable=False),
sa.Column('IsActive', sa.Boolean(), nullable=False),
sa.Column('CreatedAt', sa.DateTime(timezone=True), nullable=False),
sa.Column('UpdatedAt', sa.DateTime(timezone=True), nullable=False),
sa.PrimaryKeyConstraint('Id'),
schema='OurHouse'
)

 
Thanks in advance!

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Re: [sqlalchemy] Grouped data in a Flask/SQLAlchemy class

[mike bayer]

On 03/01/2017 10:22 PM, Greg Silverman wrote:



On Wed, Mar 1, 2017 at 8:53 PM, mike bayer > wrote:



On 03/01/2017 08:27 PM, GMS wrote:

I have the following class models:


|  class DiagnosisDetail(Model):
__tablename__ = 'vw_svc_diagnosis'
diagnosis_id = Column(String(32), primary_key=True)
first_name = Column(String(255))
last_name = Column(String(255))
mrn = Column(String(255))
dx_code = Column(String(255))
dx_id = Column(String(255), ForeignKey('dx_group.dx_id'))
diagnosisgroup = relationship("DiagnosisGroup")
dx_code_type = Column(String(255))
dx_name = Column(String(255))

__mapper_args__ = {
 "order_by":[mrn, dx_name]
   }

class DiagnosisGroup(Model):
__tablename__ = 'diagnosis_group'
dx_id = Column(String(32), primary_key=True)
mrn = Column(String(255))
dx_code = Column(String(255))
dx_code_type = Column(String(255))
dx_name = Column(String(255))
diagnosis_datetime = Column(DateTime)

__mapper_args__ = {
 "order_by":[mrn, dx_name]
   }|



where the underlying tables for DiagnosisGroup and
DiagnosisDetail are
SQL views. DiagnosisGroup is so that I can have a more succinct
view of
the data, since a patient can have the same diagnosis many
times. I am
wondering if there is a way to do this within the class structure
 instead of at the db server?


do you mean, derive a DiagnosisGroup object from a DiagnosisDetail
without running SQL?



In as much as having the ORM do the work versus the backend, I guess.



(or a list of them?)  (the answer is..sure?  just build Python code
to generate objects from a list of DiagnosisDetail objects).




Hmmm... but I don't get all the benefits of related data/data
associations via key constraints that way with a non SQLA object. For
example, I have a form that binds the Grouped records to their Detailed
records in another form utilizing the one-to-many relationship between
the two classes.



my example illustrates joining the two types of objects together in the 
same way as a relationship-bound collection would.







I do not wish to do this through any ORM

session queries, since these two classes have distinct use cases
where
they bind to wtform views. Thus, I would like to inherit the
properties
of these two classes from another distinct class.

I have not been able to find anything like this, short
of [create-column-properties-that-use-a-groupby][1]

>,
but this uses session queries to achieve the result. I would like to
keep everything within the class itself through inheritance of the
DiagnosisDetail class.


You don't need a relational database to do grouping, if you have a
list of data in memory it can be grouped using sets, or most
succinctly Python's own groupby function:
https://docs.python.org/2/library/itertools.html#itertools.groupby





Indeed. I have used this for other things, but never thought of it for
this case.









Note: the primary key for DiagnosisGroup, is a concatenation of
dx_code
and another field patient_id. Groupings thus are unique.


OK, so

def keyfunc(detail):
return (detail.dx_code, detail.patient_id)

def get_diagnosis_groups(sorted_list_of_diagnosis_detail):

for (dx_code, patient_id), details in
itertools.groupby(sorted_list_of_diagnosisdetail, keyfunc):
diagnosis_group = DiagnosisGroup(
   dx_code, patient_id
)
diagnosis_group.details = details
for detail in details:
detail.group = diagnosis_group
yield diagnosis_group




Is there a way to use these as methods within a class model using the
mapper, like in the stackoverflow link I gave?


this functionality can be placed on a @property on your class, can be 
done bidirectionally too.If you want a DiagnosisGroup to have a 
collection of all the DiagnosisDetails on it you'd need to find a place 
to stash the collection of all the DD objects you're dealing with in memory.






Thanks for the out-of-the-box approach to thinking about this.

Greg--

Re: [sqlalchemy] Grouped data in a Flask/SQLAlchemy class

[Greg Silverman]

On Wed, Mar 1, 2017 at 8:53 PM, mike bayer  wrote:

>
>
> On 03/01/2017 08:27 PM, GMS wrote:
>
>> I have the following class models:
>>
>>
>> |  class DiagnosisDetail(Model):
>> __tablename__ = 'vw_svc_diagnosis'
>> diagnosis_id = Column(String(32), primary_key=True)
>> first_name = Column(String(255))
>> last_name = Column(String(255))
>> mrn = Column(String(255))
>> dx_code = Column(String(255))
>> dx_id = Column(String(255), ForeignKey('dx_group.dx_id'))
>> diagnosisgroup = relationship("DiagnosisGroup")
>> dx_code_type = Column(String(255))
>> dx_name = Column(String(255))
>>
>> __mapper_args__ = {
>>  "order_by":[mrn, dx_name]
>>}
>>
>> class DiagnosisGroup(Model):
>> __tablename__ = 'diagnosis_group'
>> dx_id = Column(String(32), primary_key=True)
>> mrn = Column(String(255))
>> dx_code = Column(String(255))
>> dx_code_type = Column(String(255))
>> dx_name = Column(String(255))
>> diagnosis_datetime = Column(DateTime)
>>
>> __mapper_args__ = {
>>  "order_by":[mrn, dx_name]
>>}|
>>
>>
>>
>> where the underlying tables for DiagnosisGroup and DiagnosisDetail are
>> SQL views. DiagnosisGroup is so that I can have a more succinct view of
>> the data, since a patient can have the same diagnosis many times. I am
>> wondering if there is a way to do this within the class structure
>>  instead of at the db server?
>>
>
> do you mean, derive a DiagnosisGroup object from a DiagnosisDetail without
> running SQL?



In as much as having the ORM do the work versus the backend, I guess.



> (or a list of them?)  (the answer is..sure?  just build Python code to
> generate objects from a list of DiagnosisDetail objects).
>



Hmmm... but I don't get all the benefits of related data/data associations
via key constraints that way with a non SQLA object. For example, I have a
form that binds the Grouped records to their Detailed records in another
form utilizing the one-to-many relationship between the two classes.



>
> I do not wish to do this through any ORM
>
>> session queries, since these two classes have distinct use cases where
>> they bind to wtform views. Thus, I would like to inherit the properties
>> of these two classes from another distinct class.
>>
>> I have not been able to find anything like this, short
>> of [create-column-properties-that-use-a-groupby][1]
>> > e-column-properties-that-use-a-groupby/25879453>,
>> but this uses session queries to achieve the result. I would like to
>> keep everything within the class itself through inheritance of the
>> DiagnosisDetail class.
>>
>
> You don't need a relational database to do grouping, if you have a list of
> data in memory it can be grouped using sets, or most succinctly Python's
> own groupby function: https://docs.python.org/2/libr
> ary/itertools.html#itertools.groupby




Indeed. I have used this for other things, but never thought of it for this
case.




>
>
>
>
>
>> Note: the primary key for DiagnosisGroup, is a concatenation of dx_code
>> and another field patient_id. Groupings thus are unique.
>>
>
> OK, so
>
> def keyfunc(detail):
> return (detail.dx_code, detail.patient_id)
>
> def get_diagnosis_groups(sorted_list_of_diagnosis_detail):
>
> for (dx_code, patient_id), details in
> itertools.groupby(sorted_list_of_diagnosisdetail, keyfunc):
> diagnosis_group = DiagnosisGroup(
>dx_code, patient_id
> )
> diagnosis_group.details = details
> for detail in details:
> detail.group = diagnosis_group
> yield diagnosis_group
>



Is there a way to use these as methods within a class model using the
mapper, like in the stackoverflow link I gave?

Thanks for the out-of-the-box approach to thinking about this.

Greg--



>
>
>
> I do also need
>
>> the FK relation back to the DiagnosisDetail class, which leads me to
>> believe there should be three classes, where the two above classes
>> inherit their properties from a parent class.
>>
>
>
>
>
>
>> --
>> SQLAlchemy -
>> The Python SQL Toolkit and Object Relational Mapper
>>
>> http://www.sqlalchemy.org/
>>
>> To post example code, please provide an MCVE: Minimal, Complete, and
>> Verifiable Example. See http://stackoverflow.com/help/mcve for a full
>> description.
>> ---
>> You received this message because you are subscribed to the Google
>> Groups "sqlalchemy" group.
>> To unsubscribe from this group and stop receiving emails from it, send
>> an email to sqlalchemy+unsubscr...@googlegroups.com
>> .
>> To post to this group, send email to sqlalchemy@googlegroups.com
>> .
>> Visit this group at 

Re: [sqlalchemy] Sqlalchemy is showing the wrong database tables

[mike bayer]

try running the MySQL command line client:

mysql -u root -h localhost salestax

then do "show tables".  that will show you what tables are in the 
"salestax" database.




On 03/01/2017 08:31 PM, Wilfredo Rivera wrote:

I am trying to connect to MySQL database with sqlalchemy. The connection
is succesful, but when I query the tables of the database it shows me
the wrong tables. The tables that the script shows are the ones that I
see in the MySQL for Excel extension, but not the one that is in
database that I want to connect to. The schemas showed in the MySQL for
Excel extension are different that the models that I see in the MySQL
workbench, but I don't know why.


How can I debug this problem?


|DB_USER ='root'DB_PASSWORD =''DB_HOST ='localhost'DB_MODEL
='salestax'connection_string
="mysql+pymysql://{}:{}@{}/{}".format(DB_USER,DB_PASSWORD,DB_‌​
HOST,DB_MODEL)engine =create_engine(connection_string)connection
=engine.connect()print(engine.table_names())|

|I will appreciate the help. I am a beginner trying to code a simple
application, but this got me stuck.|

|
|

--
SQLAlchemy -
The Python SQL Toolkit and Object Relational Mapper

http://www.sqlalchemy.org/

To post example code, please provide an MCVE: Minimal, Complete, and
Verifiable Example. See http://stackoverflow.com/help/mcve for a full
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http://www.sqlalchemy.org/

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Re: [sqlalchemy] Grouped data in a Flask/SQLAlchemy class

[mike bayer]

On 03/01/2017 08:27 PM, GMS wrote:

I have the following class models:


|  class DiagnosisDetail(Model):
__tablename__ = 'vw_svc_diagnosis'
diagnosis_id = Column(String(32), primary_key=True)
first_name = Column(String(255))
last_name = Column(String(255))
mrn = Column(String(255))
dx_code = Column(String(255))
dx_id = Column(String(255), ForeignKey('dx_group.dx_id'))
diagnosisgroup = relationship("DiagnosisGroup")
dx_code_type = Column(String(255))
dx_name = Column(String(255))

__mapper_args__ = {
 "order_by":[mrn, dx_name]
   }

class DiagnosisGroup(Model):
__tablename__ = 'diagnosis_group'
dx_id = Column(String(32), primary_key=True)
mrn = Column(String(255))
dx_code = Column(String(255))
dx_code_type = Column(String(255))
dx_name = Column(String(255))
diagnosis_datetime = Column(DateTime)

__mapper_args__ = {
 "order_by":[mrn, dx_name]
   }|



where the underlying tables for DiagnosisGroup and DiagnosisDetail are
SQL views. DiagnosisGroup is so that I can have a more succinct view of
the data, since a patient can have the same diagnosis many times. I am
wondering if there is a way to do this within the class structure
 instead of at the db server?


do you mean, derive a DiagnosisGroup object from a DiagnosisDetail 
without running SQL? (or a list of them?)  (the answer is..sure?  just 
build Python code to generate objects from a list of DiagnosisDetail 
objects).


I do not wish to do this through any ORM

session queries, since these two classes have distinct use cases where
they bind to wtform views. Thus, I would like to inherit the properties
of these two classes from another distinct class.

I have not been able to find anything like this, short
of [create-column-properties-that-use-a-groupby][1]
,
but this uses session queries to achieve the result. I would like to
keep everything within the class itself through inheritance of the
DiagnosisDetail class.


You don't need a relational database to do grouping, if you have a list 
of data in memory it can be grouped using sets, or most succinctly 
Python's own groupby function: 
https://docs.python.org/2/library/itertools.html#itertools.groupby






Note: the primary key for DiagnosisGroup, is a concatenation of dx_code
and another field patient_id. Groupings thus are unique.


OK, so

def keyfunc(detail):
return (detail.dx_code, detail.patient_id)

def get_diagnosis_groups(sorted_list_of_diagnosis_detail):

for (dx_code, patient_id), details in 
itertools.groupby(sorted_list_of_diagnosisdetail, keyfunc):

diagnosis_group = DiagnosisGroup(
   dx_code, patient_id
)
diagnosis_group.details = details
for detail in details:
detail.group = diagnosis_group
yield diagnosis_group




I do also need

the FK relation back to the DiagnosisDetail class, which leads me to
believe there should be three classes, where the two above classes
inherit their properties from a parent class.







--
SQLAlchemy -
The Python SQL Toolkit and Object Relational Mapper

http://www.sqlalchemy.org/

To post example code, please provide an MCVE: Minimal, Complete, and
Verifiable Example. See http://stackoverflow.com/help/mcve for a full
description.
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http://www.sqlalchemy.org/

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[sqlalchemy] Sqlalchemy is showing the wrong database tables

[Wilfredo Rivera]

I am trying to connect to MySQL database with sqlalchemy. The connection is 
succesful, but when I query the tables of the database it shows me the 
wrong tables. The tables that the script shows are the ones that I see in 
the MySQL for Excel extension, but not the one that is in database that I 
want to connect to. The schemas showed in the MySQL for Excel extension are 
different that the models that I see in the MySQL workbench, but I don't 
know why.


How can I debug this problem?


DB_USER = 'root' 
DB_PASSWORD = '' 
DB_HOST = 'localhost' 
DB_MODEL = 'salestax' 
connection_string = 
"mysql+pymysql://{}:{}@{}/{}".format(DB_USER,DB_PASSWORD,DB_‌​HOST, DB_MODEL) 
engine = create_engine(connection_string) 
connection = engine.connect()   print(engine.table_names())

I will appreciate the help. I am a beginner trying to code a simple 
application, but this got me stuck.


-- 
SQLAlchemy - 
The Python SQL Toolkit and Object Relational Mapper

http://www.sqlalchemy.org/

To post example code, please provide an MCVE: Minimal, Complete, and Verifiable 
Example.  See  http://stackoverflow.com/help/mcve for a full description.
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[sqlalchemy] Grouped data in a Flask/SQLAlchemy class

[GMS]

I have the following class models:

  
  class DiagnosisDetail(Model):
__tablename__ = 'vw_svc_diagnosis'
diagnosis_id = Column(String(32), primary_key=True)
first_name = Column(String(255))
last_name = Column(String(255))
mrn = Column(String(255))
dx_code = Column(String(255))
dx_id = Column(String(255), ForeignKey('dx_group.dx_id'))
diagnosisgroup = relationship("DiagnosisGroup")
dx_code_type = Column(String(255))
dx_name = Column(String(255))

__mapper_args__ = {
 "order_by":[mrn, dx_name]
   }

class DiagnosisGroup(Model):
__tablename__ = 'diagnosis_group'
dx_id = Column(String(32), primary_key=True)
mrn = Column(String(255))
dx_code = Column(String(255))
dx_code_type = Column(String(255))
dx_name = Column(String(255))
diagnosis_datetime = Column(DateTime)

__mapper_args__ = {
 "order_by":[mrn, dx_name]
   }



where the underlying tables for DiagnosisGroup and DiagnosisDetail are SQL 
views. DiagnosisGroup is so that I can have a more succinct view of the 
data, since a patient can have the same diagnosis many times. I am 
wondering if there is a way to do this within the class structure  instead 
of at the db server? I do not wish to do this through any ORM session 
queries, since these two classes have distinct use cases where they bind to 
wtform views. Thus, I would like to inherit the properties of these two 
classes from another distinct class. 

I have not been able to find anything like this, short of 
[create-column-properties-that-use-a-groupby][1] 
,
 
but this uses session queries to achieve the result. I would like to keep 
everything within the class itself through inheritance of the 
DiagnosisDetail class.

Note: the primary key for DiagnosisGroup, is a concatenation of dx_code and 
another field patient_id. Groupings thus are unique. I do also need the FK 
relation back to the DiagnosisDetail class, which leads me to believe there 
should be three classes, where the two above classes inherit their 
properties from a parent class.

-- 
SQLAlchemy - 
The Python SQL Toolkit and Object Relational Mapper

http://www.sqlalchemy.org/

To post example code, please provide an MCVE: Minimal, Complete, and Verifiable 
Example.  See  http://stackoverflow.com/help/mcve for a full description.
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[sqlalchemy] Grouped data in a Flask/SQLAlchemy class

[GMS]

I have the following class models:

  
  class DiagnosisDetail(Model):
__tablename__ = 'vw_svc_diagnosis'
diagnosis_id = Column(String(32), primary_key=True)
first_name = Column(String(255))
last_name = Column(String(255))
mrn = Column(String(255))
dx_code = Column(String(255))
dx_id = Column(String(255), ForeignKey('dx_group.dx_id'))
diagnosisgroup = relationship("DiagnosisGroup")
dx_code_type = Column(String(255))
dx_name = Column(String(255))

__mapper_args__ = {
 "order_by":[mrn, dx_name]
   }

class DiagnosisGroup(Model):
__tablename__ = 'diagnosis_group'
dx_id = Column(String(32), primary_key=True)
mrn = Column(String(255))
dx_code = Column(String(255))
dx_code_type = Column(String(255))
dx_name = Column(String(255))
diagnosis_datetime = Column(DateTime)

__mapper_args__ = {
 "order_by":[mrn, dx_name]
   }



where the underlying tables for DiagnosisGroup and DiagnosisDetail, 
diagnosis_group, are SQL views. DiagnosisGroup is so that I can have a more 
succinct view of the data, since a patient can have the same dx_code many 
times. I am wondering if there is a way to do this within the class 
structure for , instead of at the db server? I do not wish to do this 
through any ORM session queries, since these two classes have distinct use 
cases where they bind to wtform views. Thus, I would like to inherit the 
properties of these two classes from another distinct class. 

I have not been able to find anything like this, short of 
[create-column-properties-that-use-a-groupby][1] 
,
 
but this uses session queries to achieve the result. I would like to keep 
everything within the class itself through inheritance of the 
DiagnosisDetail class.

Note: the primary key for DiagnosisGroup, is a concatenation of dx_code and 
another field patient_id. Groupings thus are unique. I do also need the FK 
relation back to the DiagnosisDetail class, which leads me to believe there 
should be three classes, where the two above classes inherit their 
properties from a parent class.

-- 
SQLAlchemy - 
The Python SQL Toolkit and Object Relational Mapper

http://www.sqlalchemy.org/

To post example code, please provide an MCVE: Minimal, Complete, and Verifiable 
Example.  See  http://stackoverflow.com/help/mcve for a full description.
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[sqlalchemy] Alembic 0.9.1 released

[mike bayer]

Alembic release 0.9.1 is now available.

One improvement from 0.9.0, regarding raising when a migration 
inadvertently left an internal transaction open, had an unintended side 
effect for some custom env.py environments; the issue has been fixed.


Changelog is at: 
http://alembic.zzzcomputing.com/en/latest/changelog.html#change-0.9.1


Download Alembic 0.9.1 at:  https://pypi.python.org/pypi/alembic

--
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The Python SQL Toolkit and Object Relational Mapper


http://www.sqlalchemy.org/

To post example code, please provide an MCVE: Minimal, Complete, and Verifiable 
Example.  See  http://stackoverflow.com/help/mcve for a full description.
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