Re: SMILES Proto Schema
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 Date: Thursday, June 16, 2022 at 12:16 PM To: dev@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
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 > 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 <mailto:asanabhav...@gmail.com>> > Date: Monday, June 20, 2022 at 9:16 AM > To: dev@airavata.apache.org <mailto:dev@airavata.apache.org> > mailto:dev@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
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
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 Date: Monday, June 20, 2022 at 9:16 AM To: dev@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
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
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 calc_properties.proto Description: Binary data calc_topology.proto Description: Binary data calc_info.proto Description: Binary data molecule.proto Description: Binary data
