Grouped data in a Flask/SQLAlchemy class

GMS

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Mar 1, 2017, 8:27:04 PM3/1/17

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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.

mike bayer

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Mar 1, 2017, 9:53:53 PM3/1/17

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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]

> <http://stackoverflow.com/questions/25822393/how-can-i-create-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/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
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Greg Silverman

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Mar 1, 2017, 10:23:03 PM3/1/17

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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]
<http://stackoverflow.com/questions/25822393/how-can-i-create-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/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?

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.
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mike bayer

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Mar 1, 2017, 10:52:41 PM3/1/17

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

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--
>
>
>
>
>
>
> 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
> <http://stackoverflow.com/help/mcve> for a full
> description.
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>
> --
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>
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>
> To post example code, please provide an MCVE: Minimal, Complete, and
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>
> --
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>
> › flora-script <http://flora-script.grenzi.org/> ‹
> * *› grenzi.org <http://grenzi.org/> ›

>
> --
> SQLAlchemy -
> The Python SQL Toolkit and Object Relational Mapper
>
> http://www.sqlalchemy.org/
>
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Greg Silverman

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Mar 2, 2017, 2:14:34 PM3/2/17

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Mike,

I'll try it and let you know the outcome (it may be a bit before I get to it, but I like your suggestions much better than having to use SQL views, which I am only doing due to a time crunch).

Much appreciated!

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Greg Silverman

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Apr 24, 2017, 12:51:43 PM4/24/17

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Hi Mike,

I'm finally getting to this. Instead of having both a detail and grouped methods, I would like to have only the grouped method. I'm not sure I follow your suggestion for the two methods above and how that would be modified to fit into the @property in my class.

Could you please elaborate a bit how these would work within context of the class?

Thanks!

Greg--

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mike bayer

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Apr 24, 2017, 1:21:24 PM4/24/17

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On 04/24/2017 12:51 PM, Greg Silverman wrote:
> Hi Mike,
> I'm finally getting to this. Instead of having both a detail and
> grouped methods, I would like to have only the grouped method. I'm not
> sure I follow your suggestion for the two methods above and how that
> would be modified to fit into the @property in my class.
>
> Could you please elaborate a bit how these would work within context of
> the class?

cutting and pasting:

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

you want to take out the "sorted_list_of_diagnosis_detail" argument.
OK....but I don't know where you'd like to get this from. Where is this
"method" going and are you calling that as a classmethod or an instance
method? what class? Just show a usage example.

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>
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Greg Silverman

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Apr 24, 2017, 3:42:05 PM4/24/17

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My naive first response would be that I want the class to look like

class DiagnosisTest(Model):
    __tablename__ = 'vw_svc_diagnosis'
    #id = Column(Integer, primary_key=True, autoincrement=True)
    dx_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_code_orig = Column(String(255))

    dx_code_type = Column(String(255))
    dx_name = Column(String(255))

    #chronic_diagnosis_yn = Column(String(255))
    diagnosis_datetime = Column(DateTime)



    @property
    def get_diagnosis_groups(self):

        import itertools as itertools

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

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

So that I could then instantiate this and access grouped elements like DiagnosisTest.get_diagnosis_groups.patient_id and DiagnosisTest.get_diagnosis_groups.dx_code for example.

I am sure this does not answer your question, but what I really want to do is have the data grouped within the class and available whenever I instantiate the class.

I know what I need, but I am having problems in articulating the details.

Thanks for being patient with me! ^_^

Thanks!

Greg--

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mike bayer

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Apr 24, 2017, 4:06:37 PM4/24/17

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On 04/24/2017 03:42 PM, Greg Silverman wrote:
> My naive first response would be that I want the class to look like
>
> class DiagnosisTest(Model):

> __tablename__= 'vw_svc_diagnosis'

> #id = Column(Integer, primary_key=True, autoincrement=True)
> dx_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_code_orig = Column(String(255))
> dx_code_type= Column(String(255))
> dx_name= Column(String(255))
> #chronic_diagnosis_yn = Column(String(255))

> diagnosis_datetime= Column(DateTime)

>
>
>
> @property
> def get_diagnosis_groups(self):
>
> import itertoolsas itertools
>

> for (dx_code, patient_id), detailsin itertools.groupby(self, keyfunc):

> diagnosis_group = DiagnosisGroup(
> dx_code, patient_id
> )
> diagnosis_group.details= details
> for detailin details:

> detail.group= diagnosis_group

> yield diagnosis_group
>
>
> So that I could then instantiate this and access grouped elements like
> DiagnosisTest.get_diagnosis_groups.patient_id and
> DiagnosisTest.get_diagnosis_groups.dx_code for example.

OK can you add a relationship() to DiagnosisTest that returns a list of
DiagnosisDetail objects? that would be all you need here.

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>
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>
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>
> To post example code, please provide an MCVE: Minimal, Complete,
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Greg Silverman

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Apr 24, 2017, 4:32:53 PM4/24/17

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Yes, I can certainly do that. Sounds pretty simple, actually. I may have more questions as I dive into this.

Thanks!

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http://www.sqlalchemy.org/

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