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Posted to dev@airavata.apache.org by Bhavesh Asanabada <as...@gmail.com> on 2022/06/16 16:14:46 UTC
SMILES Proto Schema
Hi Sudhakar,
I’ve done with the sample gRPC implementation. As a next step towards the
GSoC goal, I’m structuring the proto buffer files considering the files you
have shared before (attached with this mail).
Proceeding with the files, there are a few missing data types in the
molecule.proto file which I could not figure out with the variables
mentioned. Can you please confirm the data types? and suggest the
additional changes you need in the schema.
Thanks
Bhavesh Asanabada
Re: SMILES Proto Schema
Posted by Bhavesh Asanabada <as...@gmail.com>.
Hi Sudhakar,
The error is because of version incompatibility. I used the Java compiler
of version 18. I suggest installing the same version for the future build
or you can change to your version in the pom.xml file (line 17).
*pom file path: *cd ~/airavata-sandbox/gsoc2022/smilesdb/Server/pom.xml
Also for executing DjangoMiddleware, you need python version 3.8.3 for
running the grpcio-wheel. Please look for the specific version at
https://www.python.org/downloads/.
[image: image.png]
Thanks,
Bhavesh Asanabada
On Fri, Jul 29, 2022 at 1:56 AM Pamidighantam, Sudhakar V <
spamidig@illinois.edu> wrote:
> Bhavesh:
>
>
>
> When I tried to run java package I got this error.
>
>
>
> Do you know what could be missing?
>
>
>
> Thanks,
>
> Sudhakar.
>
>
>
> [*INFO*] Changes detected - recompiling the module!
>
> [*INFO*] Compiling 38 source files to
> /Users/spamidig/Library/Applications/smilesdb/airavata-sandbox/gsoc2022/smilesdb/Server/target/classes
>
> [*INFO*]
> *------------------------------------------------------------------------*
>
> [*INFO*] *BUILD FAILURE*
>
> [*INFO*]
> *------------------------------------------------------------------------*
>
> [*INFO*] Total time: 16.819 s
>
> [*INFO*] Finished at: 2022-07-28T16:20:45-04:00
>
> [*INFO*]
> *------------------------------------------------------------------------*
>
> [*ERROR*] Failed to execute goal
> org.apache.maven.plugins:maven-compiler-plugin:3.10.1:compile
> *(default-compile)* on project Server: *Fatal error compiling*: error:
> invalid target release: 18 -> *[Help 1]*
>
> [*ERROR*]
>
> [*ERROR*] To see the full stack trace of the errors, re-run Maven with
> the *-e* switch.
>
> [*ERROR*] Re-run Maven using the *-X* switch to enable full debug logging.
>
> [*ERROR*]
>
> [*ERROR*] For more information about the errors and possible solutions,
> please read the following articles:
>
> [*ERROR*] *[Help 1]*
> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>
>
>
>
>
> *From: *Bhavesh Asanabada <as...@gmail.com>
> *Date: *Thursday, June 16, 2022 at 12:16 PM
> *To: *dev@airavata.apache.org <de...@airavata.apache.org>
> *Subject: *SMILES Proto Schema
>
> Hi Sudhakar,
> I’ve done with the sample gRPC implementation. As a next step towards the
> GSoC goal, I’m structuring the proto buffer files considering the files you
> have shared before (attached with this mail).
>
> Proceeding with the files, there are a few missing data types in the
> molecule.proto file which I could not figure out with the variables
> mentioned. Can you please confirm the data types? and suggest the
> additional changes you need in the schema.
>
> Thanks
> Bhavesh Asanabada
>
Re: SMILES Proto Schema
Posted by "Pamidighantam, Sudhakar V" <sp...@illinois.edu>.
Bhavesh:
When I tried to run java package I got this error.
Do you know what could be missing?
Thanks,
Sudhakar.
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 38 source files to /Users/spamidig/Library/Applications/smilesdb/airavata-sandbox/gsoc2022/smilesdb/Server/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 16.819 s
[INFO] Finished at: 2022-07-28T16:20:45-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.10.1:compile (default-compile) on project Server: Fatal error compiling: error: invalid target release: 18 -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
From: Bhavesh Asanabada <as...@gmail.com>
Date: Thursday, June 16, 2022 at 12:16 PM
To: dev@airavata.apache.org <de...@airavata.apache.org>
Subject: SMILES Proto Schema
Hi Sudhakar,
I’ve done with the sample gRPC implementation. As a next step towards the GSoC goal, I’m structuring the proto buffer files considering the files you have shared before (attached with this mail).
Proceeding with the files, there are a few missing data types in the molecule.proto file which I could not figure out with the variables mentioned. Can you please confirm the data types? and suggest the additional changes you need in the schema.
Thanks
Bhavesh Asanabada
Re: SMILES Proto Schema
Posted by Suresh Marru <sm...@apache.org>.
I suggest we use a system generated unique ID as the primary key and SMILES Strings as an optional queryable file.
Yes a call to demonstrate is fine. Let's coordinate on a time on Airavata slack channel.
Suresh
> On Jun 20, 2022, at 10:22 AM, Pamidighantam, Sudhakar V <sp...@illinois.edu> wrote:
>
> Bhavesh:
>
> We need to pick a primary key. SMILES string could be a good one but is not absolutely needed to be. Also sometimes it is difficult to auto-generate SMILES strings for molecules. We can choose another one such as name but we need to consistently and uniquely use the name across data models.
> The filtering should get all the records and we can have pagination to control how many are shown. Some options in the filters could include ranges for example, Absorption Max between 500-560nm.
>
> Thanks,
> Sudhakar.
> From: Bhavesh Asanabada <asanabhavesh@gmail.com <ma...@gmail.com>>
> Date: Monday, June 20, 2022 at 9:16 AM
> To: dev@airavata.apache.org <ma...@airavata.apache.org> <dev@airavata.apache.org <ma...@airavata.apache.org>>
> Subject: Re: SMILES Proto Schema
>
> Hi Sudhakar,
>
> I have a few doubts;
> I don't find the primary key (the SMILES string) in other proto files. Do I need to include it and access the data with the SMILES string?
> In the filtering options, Are there any predefined thresholds for the quantities?
> I also request to have a meeting to confirm with my SMILES query code.
>
> Thanks & Regards
> Bhavesh Asanabada
Re: SMILES Proto Schema
Posted by Bhavesh Asanabada <as...@gmail.com>.
Hi Sudhakar,
Thank you for the confirmation.
As of now, I have implemented an end-to-end MongoDB integration of one
proto file (i.e., calc_info.proto).
I request Sudhakar or Suresh to have a meeting to demonstrate the code and
get your feedback to work on other proto files.
Thanks
Bhavesh Asanabada.
Re: SMILES Proto Schema
Posted by "Pamidighantam, Sudhakar V" <sp...@illinois.edu>.
Bhavesh:
1. We need to pick a primary key. SMILES string could be a good one but is not absolutely needed to be. Also sometimes it is difficult to auto-generate SMILES strings for molecules. We can choose another one such as name but we need to consistently and uniquely use the name across data models.
2. The filtering should get all the records and we can have pagination to control how many are shown. Some options in the filters could include ranges for example, Absorption Max between 500-560nm.
Thanks,
Sudhakar.
From: Bhavesh Asanabada <as...@gmail.com>
Date: Monday, June 20, 2022 at 9:16 AM
To: dev@airavata.apache.org <de...@airavata.apache.org>
Subject: Re: SMILES Proto Schema
Hi Sudhakar,
I have a few doubts;
1. I don't find the primary key (the SMILES string) in other proto files. Do I need to include it and access the data with the SMILES string?
2. In the filtering options, Are there any predefined thresholds for the quantities?
I also request to have a meeting to confirm with my SMILES query code.
Thanks & Regards
Bhavesh Asanabada
Re: SMILES Proto Schema
Posted by Bhavesh Asanabada <as...@gmail.com>.
Hi Sudhakar,
I have a few doubts;
1. I don't find the primary key (the SMILES string) in other
proto files. Do I need to include it and access the data with the SMILES
string?
2. In the filtering options, Are there any predefined thresholds for the
quantities?
I also request to have a meeting to confirm with my SMILES query code.
Thanks & Regards
Bhavesh Asanabada
Re: SMILES Proto Schema
Posted by "Pamidighantam, Sudhakar" <pa...@iu.edu>.
Bhavesh:
The molfile is a molfile type or mol2 file type, see attached, or
???? molfile_blob ; //mediumblob
??? molecule_serialized ; //mediumblob // this is a serialized form of the previous one
??? gif_file ; //mediumblob //this is an image dif type https://helpx.adobe.com/photoshop-elements/using/optimizing-images-gif-or-png.html
??? svg_file ; //mediumblob // this is an image svg type https://www.w3.org/TR/SVG11/
Thanks,
Sudhakar.
From: Bhavesh Asanabada <as...@gmail.com>
Reply-To: "dev@airavata.apache.org" <de...@airavata.apache.org>
Date: Thursday, June 16, 2022 at 12:16 PM
To: "dev@airavata.apache.org" <de...@airavata.apache.org>
Subject: SMILES Proto Schema
Hi Sudhakar,
I’ve done with the sample gRPC implementation. As a next step towards the GSoC goal, I’m structuring the proto buffer files considering the files you have shared before (attached with this mail).
Proceeding with the files, there are a few missing data types in the molecule.proto file which I could not figure out with the variables mentioned. Can you please confirm the data types? and suggest the additional changes you need in the schema.
Thanks
Bhavesh Asanabada