Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
Is the project plan strong enough in the hibernate part modifications and
implementations?
I am going to distribute it in the timeline and posting the proposal by
tonight or tomorrow.

Regards,
Prateek


On Mon, Apr 29, 2013 at 11:48 AM, <nl...@us...> wrote:

> Hi Prateek,
>
> thank you for the detailed implementation ideas regarding the project.
>
>
> Regards,
>   Nils
>
>
> On Monday 29 April 2013 03:38:00 Prateek Gupta wrote:
> > hi,
> > This is the project details I have figured out with the tentative
> necessary
> > classes and fucntion needed to be built. If you could review them and
> > suggest me the changes.
> >
> > Project plan details
> > The project would include the development of some java classes and
> > functions the detail info of which has been provided as below:
> > Phase I
> > A)Download of the JChemPaint and its dependencies
> > 1)The project seeks to initially embedd the JChemPaint application into
> the
> > ScaffoldHunter project making it the structure editor and satisfy the
> > dependencies.Firstly to download and store the JChemPaint.jar file in a
> > separate folder named "JChemPaint" in the library of ScaffoldHunter.Then
> > the major dependency being the Chemistry Development Kit(CDK).This needs
> to
> > be taken care of.
> >
> > 2)The CDK is already loaded in the ScaffoldHunter project in the lib/cdk
> > folder.Hence the next target is to alter the configuration of the build
> of
> > the JChemPaint so as to configure the path to the CDK.For this, the
> target
> > file is the build.xml file.This can be altered by altering the
> > (approximately) lines 43 - 153 and lines 306 - 353 in the build.xml file
> > and setting the proper ids and names.
> >
> > 3)Apart from this, Apache maven-which is a build automation tool similar
> to
> > ant, needs to be imported as it facilitates the XML files to describe the
> > build. It is written in java and is required for proper build of
> JChemPaint.
> >
> > B)changes in the filter module
> > Development of a class JCP
> > This class would handle the overall activities and functions related to
> the
> > JChemPaint editor code and different files.They have been described as
> > under.
> > 1)constructor JCP()
> > The variables required would be declared and would be initialized with
> the
> > default value in this part.Their scope would be decided and worked
> > accordingly.
> >
> > 2)function calljcp()
> > *)Addition of a button for providing as a link to the JChemPaint editor
> in
> > the filter panel in the edu/udo/scaffoldhunter/model/db.This would call
> the
> > JCP class and its different functions .This would require Java GUI
> coding.
> > The jchempaint.jar can directly be called in the running program by
> > building the class path properly and importing them in the program.
> >
> > *)After this the editor would start and the user will be able to edit the
> > molecular structure as per requirement.The file containing the structure
> > would be created. The MDL mol format structure so created can be directly
> > imported as an object instance to the filtering framework and used.This
> > structure would be converted to the feature and rules format by the use
> of
> > scaffoldhunter/model/datacalculation/DBMoleculeToCDKMoleculeTransform.
> >
> > 4)finally all these functions would be called in the main before the
> > filtering procedure begins and the user entered query will be considered
> > with the subset value that is in the current framework.The normal
> procedure
> > would be resumed from hereon.
> >
> > Phase II
> > Modifications in the Hibernate
> > There is no direct support for bitwise operations in the hibernate
> > associated to the problem but there is a workaround that cannot be
> > standardised for any database present but can be standardised for the
> > databases being used by specific softwares. I propose the plan to modify
> > the mysql and hsql dialect files in the embedded hibernate library.The
> > classes will be created in both the dialects i.e.MySQLDialect and
> > HSQLDialect.
> >
> > 1)The project requires development of SQLFunctionTemplates on the
> > respective dialect subclasses.This requires analysing and maintaining
> > record of the various queries that are facing the problem and
> categorising
> > them in terms of the bitwise operator requirement and to develop that
> many
> > SQLFunctionTemplate as the number of categories and register them as
> > functions.
> >
> > 2)Development of a class SQLFunctionTemplate which would import
> > dialect.function.VARARGSQLFunction and implement SQLFunction class. The
> > import of the  dialect.function is for registering the template functions
> > and implementing SQLFunction is because SQLFunction class is contained in
> > it.
> > This class would comprise of the functions that would provide for the
> > different bitwise operation that would be required by the fingerprinting
> > mechanism.The tentative variables and functions that would be developed
> are:
> > *)initialization of the required variables like template1, template2,
> etc.
> >
> > *)default constructor SQLFunctionTemplate()
> > This would consist of the registeration of the custom functions that
> would
> > be built as per the needs. Sample code would be like:
> >     registerFunction("bit_",new SQLFunctionTemplate(Hibernate.Integer,
> > template))
> >
> > *)function task_*()
> > These functions would perform the task that would be associated with the
> > corresponding bit functions which the dialect is written for. There would
> > be multiple task functions depending on the bit function that are
> required
> > by the fingerprinting. After doing the computation, would be returning
> > corresponding correct value.
> >
> > These following functions are a part of the implementedSQLFunction and
> will
> > be implemented as a requirement.
> > *)function getSQLFunctionTemplate()
> > This would return the template of the sql function.
> > *)function getReturntype()
> > This would the return the return type of the template.
> > *)function render()
> > This would render the function call as SQL fragment.
> >
> > Regards,
> > Prateek
>