This is an automated email from the ASF dual-hosted git repository.
smarru pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git
commit d2260bb531df5d904b5048f8dc9606544414bc1c
Author: Bhavesh Asanabada <bhavesh@Bhavesh-MacBook.local>
AuthorDate: Mon Jul 25 11:58:02 2022 +0530
updated README
---
gsoc2022/smilesdb/README.md | 95 +++++++++++++++++++++++++--------------------
1 file changed, 52 insertions(+), 43 deletions(-)
diff --git a/gsoc2022/smilesdb/README.md b/gsoc2022/smilesdb/README.md
index 44208696..22ef8948 100644
--- a/gsoc2022/smilesdb/README.md
+++ b/gsoc2022/smilesdb/README.md
@@ -1,7 +1,7 @@
# Small Molecule Ionic Lattices (SMILES) Data Models
-
+
-
+
@@ -12,7 +12,7 @@ embedded with the new features and advanced data
visualization techniques.
**DEVELOPMENT GOALS**
1. Create a robust database to reduce the latency.
2. Redesigning the data models.
-3. Synchronising the data with a user dashboard.
+3. Synchronising the data with a user dashboard on performing experiment
successfully.
# Table of Contents
@@ -23,10 +23,9 @@ embedded with the new features and advanced data
visualization techniques.
* [Server Initialization](#server-initialization)
* [Middleware (Django Application)](#middleware-django-application)
* [Client Initialization](#client-initialization)
- * [Database](#database)
+ * [Database Management](#database-management)
* [Mongo Compass GUI](#visualize-the-data-with-mongo-compass-gui)
- * [Mongo Shell](#visualize-with-mongo-shell)
- * [Test Data](#test-data)
+ * [Mongo CLI](#visualize-with-mongo-cli)
* [References](#references)
* [The Team](#the-team)
@@ -54,7 +53,6 @@ embedded with the new features and advanced data
visualization techniques.
```commandline
git init
git clone https://github.com/bhavesh-asana/airavata-sandbox.git
- cd ~/airavata-sandbox/gsoc2022/smilesdb/
```
# How to run the project
@@ -67,40 +65,51 @@ Google Remote Procedure Call (gRPC) stub is implemented in
Java, which
acts as a server and helps to transfer the data effectively with the
connected clients across the distributed systems.
-Open the **Server** directory in IntelliJ and follow the steps to run the
-server application.
-
-1. Open the terminal in IntelliJ and ensure you are in the **Server** path.
-2. Run the following commands to build the maven project. <br />
+1. Before initializing the server, make sure the MongoDB is installed and the
instance
+ is running locally.
```commandline
- mvn clean compile install
- ```
-3. In the target folder, make the following directories as a source root.
- 1. target/classes
- 2. target/generated-sources/protobuf/grpc-java
- 3. target/generated-sources/protobuf/java
-4. Run the **ServerApplication** to initialise the server.
-5. On successful build, you can find the following message in the
terminal.<br/>
- **message:** Server running successfully<br/>
- This ensures that the server is listening at the local port 7594.
+ mongo --port 27017
+ ```
+ This command ensure the Mongo instance is running locally and connected the
instance to the port 27017.
+2. Open a new terminal window (server_runner) and change the directory to the
+ server codebase
+ ```commandline
+ cd ~/airavata-sandbox/gsoc2022/smilesdb/Server/
+ ```
+3. Build the Maven project.
+ ```commandline
+ mvn package
+ mvn clean install
+ ```
+4. Run the Spring Boot application.
+ ```commandline
+ mvn spring-boot:run
+ ```
+ On successful running of the server application, it shows a message as
+ _"Server running successfully"_ and open connection with mongodb driver.
## Middleware (Django Application)
-Open the **DjangoMiddleware** directory in Pycharm and follow the steps to run
the middleware.
-1. Create a virtual environment using the following command. <br/>
+Open a new terminal window and follow the steps to run the middleware
application.
+1. Change the working directory to SMILES middleware.
+ ```commandline
+ cd ~/airavata-sandbox/gsoc2022/smilesdb/DjangoMiddleware
+ ```
+2. Create a virtual environment using the following command. <br/>
Strictly recommended to use Python version 3.8.3 to build the
**grpcio-wheel**.
```commandline
- $ python -m venv <EnvironmentName>
- $ source <EnvironmentName>/bin/activate
+ $ conda create -n <EnvironmentName> python=3.8.3
+ $ conda activate <EnvironmentName>
```
-2. Install the required dependencies using the **requirements.txt** file.
+3. Upgrade the PIP version and install the required dependencies using the
**requirements.txt** file.
```commandline
- $ pip install requirements.txt
+ pip install -U pip
+ pip install -r requirements
```
-3. Run the Django application.
+4. Run the Django application.
```commandline
- $ python manage.py runserver
+ python manage.py runserver
```
-4. Open http://127.0.0.1:8000/api/calcinfo/ to check the data transmission from
+5. Open http://127.0.0.1:8000/api/calcinfo/ to check the data transmission from
the server application. On successful transmission, the data can also be
visualized
in the server terminal.
@@ -111,19 +120,22 @@ The vue.js is communicated with the Django application
(Middleware)
using REST api calls and the data is exchanged in between the server
and client application.
-To run the client application, follow the below steps
-1. Open the **smiles_dashboard** directory in PyCharm (another window).
+To run the client application, open a new terminal window and follow the below
steps
+1. Change the working directory to SMILES Dashboard.
+ ```commandline
+ cd ~/airavata-sandbox/gsoc2022/smilesdb/smiles_dashboard
+ ```
2. Open the new terminal and run the following commands to build the project.
```commandline
npm install
npm run serve
```
3. Open
- - http://localhost:8081/ for Login page.
- - http://localhost:8081/SEAGrid for SEAGrid Homepage.
- - http://localhost:8081/calcinfo for the live data synchronization.
+ - http://localhost:8080/ for Login page.
+ - http://localhost:8080/SEAGrid for SEAGrid Homepage.
+ - http://localhost:8080/calcinfo for the live CalcInfo data synchronization.
-## Database
+## Database Management
### Visualize the data with Mongo Compass GUI
The mongo instances are configured in the application.properties file (located
@@ -132,7 +144,7 @@ to the respective port (27017). On execution of the
**ServerApplication**,
the **smiles** database is created and the test data of _calcinfo_ is sent
to the database, which can be viewed under the **calcInfo** collection.
-### Visualize with mongo shell
+### Visualize with Mongo CLI
To view the data using Mongo shell, open the terminal and follow the commands
mentioned below.
```mongo
@@ -142,10 +154,7 @@ mentioned below.
show collections
db.calcInfo.find()
```
-## Test Data
-- The instant test data for each parameter of the **calcInfo** proto buffer is
defined in <br/>
- Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java from line 20 to
24.
-- Update the data or add new data to visualize the live data handling.
+
# References
1. **Jira Issue:** <br/>
@@ -154,6 +163,7 @@ mentioned below.
https://cwiki.apache.org/confluence/display/AIRAVATA/SMILES+Data+Models
3. **GitHub - Airavata sand-box:** <br/>
Master branch: https://github.com/apache/airavata-sandbox
+4. [**DevDocs**](dev_docs.md)
# The team
@@ -167,5 +177,4 @@ mentioned below.
## Contributor
- Bhavesh Asanabada <br/>
-
[<img
src="https://img.shields.io/badge/LinkedIn-0077B5?style=plastic&logo=linkedin&logoColor=white";
/>](https://www.linkedin.com/in/bhavesh-asana/)
\ No newline at end of file
