[airavata-sandbox] branch dependabot/maven/gsoc2022/smilesdb/Server/org.mongodb-mongo-java-driver-3.11.3 created (now 8570ccdc)
This is an automated email from the ASF dual-hosted git repository. github-bot pushed a change to branch dependabot/maven/gsoc2022/smilesdb/Server/org.mongodb-mongo-java-driver-3.11.3 in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git at 8570ccdc Bump mongo-java-driver in /gsoc2022/smilesdb/Server No new revisions were added by this update.
[airavata-sandbox] 19/26: updated README
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 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. +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. - **message:** Server running successfully - 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. +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. Strictly recommended to use Python version 3.8.3 to build the **grpcio-wheel**. ```commandline - $ python -m venv - $ source /bin/activate + $ conda create -n python=3.8.3 + $ conda activate ``` -2. Install the required dependencies using the
[airavata-sandbox] 26/26: Update README
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 9d915509adbe869b362c97fbdf4b5ae1dcb0db77 Author: Bhavesh Asanabada <62237873+bhavesh-as...@users.noreply.github.com> AuthorDate: Mon Sep 12 19:59:23 2022 +0530 Update README Changed the directory paths and reconfigured the run commands. --- gsoc2022/smilesdb/README.md | 20 ++-- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/gsoc2022/smilesdb/README.md b/gsoc2022/smilesdb/README.md index 22ef8948..a1fa8470 100644 --- a/gsoc2022/smilesdb/README.md +++ b/gsoc2022/smilesdb/README.md @@ -88,11 +88,11 @@ connected clients across the distributed systems. On successful running of the server application, it shows a message as _"Server running successfully"_ and open connection with mongodb driver. -## Middleware (Django Application) +## RPC Handler (Django Application) 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 + cd ~/airavata-sandbox/gsoc2022/smilesdb/rpc_handler ``` 2. Create a virtual environment using the following command. Strictly recommended to use Python version 3.8.3 to build the **grpcio-wheel**. @@ -109,7 +109,7 @@ Open a new terminal window and follow the steps to run the middleware applicatio ```commandline python manage.py runserver ``` -5. Open http://127.0.0.1:8000/api/calcinfo/ to check the data transmission from +5. Open http://127.0.0.1:8000/api/molecule/ to check the data transmission from the server application. On successful transmission, the data can also be visualized in the server terminal. @@ -123,17 +123,17 @@ and client application. 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 + cd ~/airavata-sandbox/gsoc2022/smilesdb/data-catalog ``` 2. Open the new terminal and run the following commands to build the project. ```commandline - npm install - npm run serve + yarn install + yarn run serve ``` 3. Open - http://localhost:8080/ for Login page. - - http://localhost:8080/SEAGrid for SEAGrid Homepage. - - http://localhost:8080/calcinfo for the live CalcInfo data synchronization. + - http://localhost:8080/home for SEAGrid Homepage. + - http://localhost:8080/search for the live data catalog. ## Database Management @@ -152,7 +152,7 @@ mentioned below. show dbs use smiles show collections - db.calcInfo.find() + db.molecule.find().pretty() ``` # References @@ -177,4 +177,4 @@ mentioned below. ## Contributor - Bhavesh Asanabada - [https://img.shields.io/badge/LinkedIn-0077B5?style=plastic=linkedin=white; />](https://www.linkedin.com/in/bhavesh-asana/) \ No newline at end of file + [https://img.shields.io/badge/LinkedIn-0077B5?style=plastic=linkedin=white; />](https://www.linkedin.com/in/bhavesh-asana/)
[airavata-sandbox] 05/26: defined api urls
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 cf320cfde0820b7c6fc3b6af066926a81989c44f
Author: Bhavesh Asanabada
AuthorDate: Mon Jul 4 06:10:57 2022 +0530
defined api urls
---
.../DjangoMiddleware/DjangoMiddleware/__init__.py | 0
.../__pycache__/__init__.cpython-38.pyc| Bin 0 -> 159 bytes
.../__pycache__/settings.cpython-38.pyc| Bin 0 -> 2513 bytes
.../__pycache__/urls.cpython-38.pyc| Bin 0 -> 998 bytes
.../__pycache__/wsgi.cpython-38.pyc| Bin 0 -> 580 bytes
.../DjangoMiddleware/DjangoMiddleware/asgi.py | 16 ++
.../DjangoMiddleware/DjangoMiddleware/settings.py | 130
.../DjangoMiddleware/DjangoMiddleware/urls.py | 22 +++
.../DjangoMiddleware/DjangoMiddleware/wsgi.py | 16 ++
.../__pycache__/calc_info_pb2.cpython-38.pyc | Bin 0 -> 1596 bytes
.../__pycache__/calc_info_pb2_grpc.cpython-38.pyc | Bin 0 -> 4065 bytes
.../smilesdb/DjangoMiddleware/calc_info_pb2.py | 47 ++
.../DjangoMiddleware/calc_info_pb2_grpc.py | 165 +
.../smilesdb/DjangoMiddleware/calcinfo/__init__.py | 0
.../calcinfo/__pycache__/__init__.cpython-38.pyc | Bin 0 -> 151 bytes
.../calcinfo/__pycache__/admin.cpython-38.pyc | Bin 0 -> 192 bytes
.../calcinfo/__pycache__/apps.cpython-38.pyc | Bin 0 -> 431 bytes
.../calcinfo/__pycache__/models.cpython-38.pyc | Bin 0 -> 189 bytes
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.../calcinfo/__pycache__/views.cpython-38.pyc | Bin 0 -> 1294 bytes
.../smilesdb/DjangoMiddleware/calcinfo/admin.py| 3 +
.../smilesdb/DjangoMiddleware/calcinfo/apps.py | 6 +
.../calcinfo/migrations/__init__.py| 0
.../migrations/__pycache__/__init__.cpython-38.pyc | Bin 0 -> 162 bytes
.../smilesdb/DjangoMiddleware/calcinfo/models.py | 3 +
.../smilesdb/DjangoMiddleware/calcinfo/tests.py| 3 +
.../smilesdb/DjangoMiddleware/calcinfo/urls.py | 7 +
.../smilesdb/DjangoMiddleware/calcinfo/views.py| 37 +
gsoc2022/smilesdb/DjangoMiddleware/db.sqlite3 | Bin 0 -> 131072 bytes
gsoc2022/smilesdb/DjangoMiddleware/manage.py | 22 +++
.../DjangoMiddleware/protos/calc_info.proto| 40 +
gsoc2022/smilesdb/DjangoMiddleware/requirements| 11 ++
32 files changed, 528 insertions(+)
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b/gsoc2022/smilesdb/DjangoMiddleware/DjangoMiddleware/__pycache__/wsgi.cpython-38.pyc
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diff --git a/gsoc2022/smilesdb/DjangoMiddleware/DjangoMiddleware/asgi.py
b/gsoc2022/smilesdb/DjangoMiddleware/DjangoMiddleware/asgi.py
new file mode 100644
index ..a8c4d0c7
--- /dev/null
+++ b/gsoc2022/smilesdb/DjangoMiddleware/DjangoMiddleware/asgi.py
@@ -0,0 +1,16 @@
+"""
+ASGI config for DjangoMiddleware project.
+
+It exposes the ASGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/4.0/howto/deployment/asgi/
+"""
+
+import os
+
+from django.core.asgi import get_asgi_application
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'DjangoMiddleware.settings')
+
+application = get_asgi_application()
diff --git a/gsoc2022/smilesdb/DjangoMiddleware/DjangoMiddleware/settings.py
b/gsoc2022/smilesdb/DjangoMiddleware/DjangoMiddleware/settings.py
[airavata-sandbox] 12/26: Updated configuration
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smarru pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git
commit e01a18e86ec55fd7cdbfa756e20172adafa111f0
Author: Bhavesh Asanabada
AuthorDate: Thu Jul 14 22:32:42 2022 +0530
Updated configuration
---
gsoc2022/smilesdb/smiles_dashboard/package.json | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/gsoc2022/smilesdb/smiles_dashboard/package.json
b/gsoc2022/smilesdb/smiles_dashboard/package.json
index ac582f16..4bdfdfb0 100644
--- a/gsoc2022/smilesdb/smiles_dashboard/package.json
+++ b/gsoc2022/smilesdb/smiles_dashboard/package.json
@@ -9,7 +9,8 @@
},
"dependencies": {
"core-js": "^3.8.3",
-"vue": "^3.2.13"
+"vue": "^3.2.13",
+"vue-router": "^4.0.13"
},
"devDependencies": {
"@babel/core": "^7.12.16",
[airavata-sandbox] 16/26: Updated README
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 905fa509fe7f8b6cf615ed901cc2f875114352b4 Author: Bhavesh Asanabada AuthorDate: Thu Jul 14 23:50:47 2022 +0530 Updated README --- gsoc2022/smilesdb/README.md | 172 +++- 1 file changed, 171 insertions(+), 1 deletion(-) diff --git a/gsoc2022/smilesdb/README.md b/gsoc2022/smilesdb/README.md index 165c960e..44208696 100644 --- a/gsoc2022/smilesdb/README.md +++ b/gsoc2022/smilesdb/README.md @@ -1 +1,171 @@ -On Build!! +# Small Molecule Ionic Lattices (SMILES) Data Models + + + + + + +This project is an experimental workspace used for the Scientific and Chemical Engineering. +This is an end to end implementation of [SEAGrid Data Catalog](https://data.seagrid.org/), +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. + +# Table of Contents + +* [Pre-requisites](#pre-requisites) + * [Technical Stack](#technical-stack) + * [Set up the code directory](#set-up-the-code-directory) +* [How to run the project](#how-to-run-the-project) + * [Server Initialization](#server-initialization) + * [Middleware (Django Application)](#middleware-django-application) + * [Client Initialization](#client-initialization) + * [Database](#database) +* [Mongo Compass GUI](#visualize-the-data-with-mongo-compass-gui) +* [Mongo Shell](#visualize-with-mongo-shell) + * [Test Data](#test-data) +* [References](#references) +* [The Team](#the-team) + +# Pre-requisites + +## Technical Stack + +| **Function** | **Language/Framework/Technology used**| +|--|---| +| Backend Microservice Implementation | 1. Spring Boot (Java) _(Suggested tool IntelliJ)_ | +| Frontend Microservice Implementation | 1. Django (Python) 2. Vue JS _(Suggested tool PyCharm)_ | +| Inter-service Communication | 1. Google Remote Procedure Calls (gRPC) 2. REST framework | +| Database Management | MongoDB (Mongo Compass) | +| Performance Testing | BloomRPC (for gRPC routing) | + +## Set up the code directory + +**Suggestion:** For the effective workspace management, use IntelliJ and PyCharm. +**Working on Mac Environment:** + +1. Open the terminal application and set the path to the home directory, + use the command `cd ~/` to move to the home directory. +2. Clone the GitHub repository and use the following commands to change + the working directory. + ```commandline +git init +git clone https://github.com/bhavesh-asana/airavata-sandbox.git +cd ~/airavata-sandbox/gsoc2022/smilesdb/ +``` + +# How to run the project + +## Server Initialization + +On the server side, Spring Boot with the Maven configuration is being used to interact with the database +and define the proto schema. To start the communication services the +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. + ```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. + **message:** Server running successfully + This ensures that the server is listening at the local port 7594. + +## 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. + Strictly recommended to use Python version 3.8.3 to build the **grpcio-wheel**. + ```commandline + $ python -m venv + $ source
[airavata-sandbox] 15/26: Added navbar component
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smarru pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git
commit 4e6589b78d6eb5ed1c9e3c598859f8dc41c5566f
Author: Bhavesh Asanabada
AuthorDate: Thu Jul 14 23:01:04 2022 +0530
Added navbar component
---
.../smiles_dashboard/src/components/SEAGrid.vue| 37 ++
1 file changed, 37 insertions(+)
diff --git a/gsoc2022/smilesdb/smiles_dashboard/src/components/SEAGrid.vue
b/gsoc2022/smilesdb/smiles_dashboard/src/components/SEAGrid.vue
index af7f29cb..ac225e81 100644
--- a/gsoc2022/smilesdb/smiles_dashboard/src/components/SEAGrid.vue
+++ b/gsoc2022/smilesdb/smiles_dashboard/src/components/SEAGrid.vue
@@ -1,4 +1,11 @@
+
+
+ SEAGrid Data Catalog
+ Search
+ Directory
Browser
+
+
Welcome to SEAGrid Data Catalog
SEAGrid Data Catalog provides a sleek web interface for you to browse
and
@@ -22,6 +29,7 @@ export default {
+
.container{
width: 70em;
height: 80em;
@@ -46,4 +54,33 @@ export default {
height: 500px;
width: 700px;
}
+.navbar{
+height: 3em;
+width:100%;
+background-color: #2C2C2C;
+display: flex;
+justify-content: space-between;
+align-items: center;
+ }
+
+ li{
+color: #edf0f1;
+text-decoration: none;
+font-size: 18px;
+ }
+
+ .navbar li{
+display: inline-block;
+padding: 0px 20px;
+ }
+
+ .navbar a{
+color: #edf0f1;
+text-decoration: none;
+transition: all 0.3s ease 0s;
+ }
+
+ .navbar a:hover{
+color: #0088a9;
+ }
\ No newline at end of file
[airavata-sandbox] 18/26: added dependency
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 996ef33baba43b509ce93738e7cfdd0538c167b4
Author: Bhavesh Asanabada
AuthorDate: Mon Jul 25 11:46:20 2022 +0530
added dependency
---
gsoc2022/smilesdb/smiles_dashboard/package.json | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gsoc2022/smilesdb/smiles_dashboard/package.json
b/gsoc2022/smilesdb/smiles_dashboard/package.json
index 4bdfdfb0..2fd31c76 100644
--- a/gsoc2022/smilesdb/smiles_dashboard/package.json
+++ b/gsoc2022/smilesdb/smiles_dashboard/package.json
@@ -8,6 +8,8 @@
"lint": "vue-cli-service lint"
},
"dependencies": {
+"@auth0/auth0-vue": "^1.0.2",
+"axios": "^0.27.2",
"core-js": "^3.8.3",
"vue": "^3.2.13",
"vue-router": "^4.0.13"
[airavata-sandbox] 14/26: updated SEAGrid home
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 d1d9c666a887aaf5ed64ea86b91b74e06d732f55 Author: Bhavesh Asanabada AuthorDate: Thu Jul 14 22:35:57 2022 +0530 updated SEAGrid home --- .../smilesdb/smiles_dashboard/src/assets/architect.png | Bin 0 -> 487800 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/gsoc2022/smilesdb/smiles_dashboard/src/assets/architect.png b/gsoc2022/smilesdb/smiles_dashboard/src/assets/architect.png new file mode 100644 index ..d7ab9b24 Binary files /dev/null and b/gsoc2022/smilesdb/smiles_dashboard/src/assets/architect.png differ
[airavata-sandbox] 13/26: updated source html
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 cd50d15cc69f40048c7639778c9bd8baf8880110 Author: Bhavesh Asanabada AuthorDate: Thu Jul 14 22:35:04 2022 +0530 updated source html --- gsoc2022/smilesdb/smiles_dashboard/public/index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gsoc2022/smilesdb/smiles_dashboard/public/index.html b/gsoc2022/smilesdb/smiles_dashboard/public/index.html index 3e5a1396..a766bb65 100644 --- a/gsoc2022/smilesdb/smiles_dashboard/public/index.html +++ b/gsoc2022/smilesdb/smiles_dashboard/public/index.html @@ -1,5 +1,5 @@ - +
[airavata-sandbox] 21/26: Masked password field
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 98d76a9b3c5191f351ba70e80b10eab377f29f72 Author: Bhavesh Asanabada AuthorDate: Mon Aug 22 17:48:07 2022 +0530 Masked password field --- gsoc2022/smilesdb/Migrations/migration.sh | 14 +++--- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gsoc2022/smilesdb/Migrations/migration.sh b/gsoc2022/smilesdb/Migrations/migration.sh index 1c312158..9d9f9210 100755 --- a/gsoc2022/smilesdb/Migrations/migration.sh +++ b/gsoc2022/smilesdb/Migrations/migration.sh @@ -1,24 +1,24 @@ -# echo 'b1h3a1v1e4s2h1' | openssl enc -aes-256-cbc -md sha512 -a -pbkdf2 -iter 10 -salt -pass pass:'test@123' +# echo '' | openssl enc -aes-256-cbc -md sha512 -a -pbkdf2 -iter 10 -salt -pass pass:'test@123' # chmod 600 ./secret.txt -# echo 'mysecretpassword' | openssl enc -base64 -e -aes-256-cbc -md sha512 -a -pbkdf2 -iter 10 -salt -pass pass:b1h3a1v1e4s2h1 > .secret.lck +# echo 'mysecretpassword' | openssl enc -base64 -e -aes-256-cbc -md sha512 -a -pbkdf2 -iter 10 -salt -pass pass: > .secret.lck -# b1h3a1v1e4s2h1 +# -> example: -pPass@123 echo creating database -mysql -uroot -pb1h3a1v1e4s2h1 -e "create database OEstorage" +mysql -uroot -p -e "create database OEstorage" echo Restoring Database -mysql -h 127.0.0.1 -uroot -pb1h3a1v1e4s2h1 OEstorage < ./data/dump_29july2022.sql +mysql -h 127.0.0.1 -uroot -p OEstorage < ./data/dump_29july2022.sql echo updating rows to replace double-quote -mysql -h 127.0.0.1 -uroot -pb1h3a1v1e4s2h1 -DOEstorage < ./data/moleculesUpdate.sql +mysql -h 127.0.0.1 -uroot -p -DOEstorage < ./data/moleculesUpdate.sql echo Generating JSON -mysql -h 127.0.0.1 -uroot -pb1h3a1v1e4s2h1 -DOEstorage < ./data/molecule.sql > ./data/molecule.temp1.json +mysql -h 127.0.0.1 -uroot -p -DOEstorage < ./data/molecule.sql > ./data/molecule.temp1.json # rm ./data/molecule.json echo Replacing 'NULL' with ""
[airavata-sandbox] branch master updated (acb0eb95 -> 9d915509)
This is an automated email from the ASF dual-hosted git repository. smarru pushed a change to branch master in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git from acb0eb95 README file updated new 0fb56458 Query SMILES Data new e7223634 Create README.md new b1320cef Added CRUD methods to MolData new 45179241 Resolved issues in calc_topology builder new cf320cfd defined api urls new 6e446b6c vue webpage new 3174daeb refactor client new bda01d7d added pom file new 4c550149 created login page new 224764ba created SEAGrid home page new a26cda17 Added router view new e01a18e8 Updated configuration new cd50d15c updated source html new d1d9c666 updated SEAGrid home new 4e6589b7 Added navbar component new 905fa509 Updated README new ec76f4c7 added stubs & code refactor new 996ef33b added dependency new d2260bb5 updated README new 60f0cd4d added migration script new 98d76a9b Masked password field new cabce699 modified files new b602ddf3 added UI components new 76c6e42b added the rpc streamline new cb4e1a20 added UI component new 9d915509 Update README The 26 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "add" were already present in the repository and have only been added to this reference. Summary of changes: gsoc2022/smilesdb/Migrations/README.md |20 + .../smilesdb/Migrations/data/dump_29july2022.sql | 18230 +++ gsoc2022/smilesdb/Migrations/data/molecule.json| 1 + gsoc2022/smilesdb/Migrations/data/molecule.sql | 1 + gsoc2022/smilesdb/Migrations/data/molecule.sql.bkp | 1 + .../smilesdb/Migrations/data/moleculesUpdate.sql | 5 + gsoc2022/smilesdb/Migrations/dropcollection.js | 3 + gsoc2022/smilesdb/Migrations/migration.sh |36 + gsoc2022/smilesdb/README | 1 - gsoc2022/smilesdb/README.md| 180 + gsoc2022/smilesdb/Server/.gitignore|33 + gsoc2022/smilesdb/Server/mvnw | 316 + gsoc2022/smilesdb/Server/mvnw.cmd | 188 + gsoc2022/smilesdb/Server/pom.xml | 118 + .../src/main/java/com/smiles/CalcInfoImpl.java | 204 + .../src/main/java/com/smiles/MoleculeImpl.java | 372 + .../java/com/smiles/SpringServerApplication.java |36 + .../smilesdb/Server/src/main/proto/calc_info.proto |85 + .../smilesdb/Server/src/main/proto/molecule.proto | 119 + .../src/main/resources/application.properties | 0 .../com/smiles/SpringServerApplicationTests.java |13 + gsoc2022/smilesdb/data-catalog/README.md |24 + gsoc2022/smilesdb/data-catalog/babel.config.js | 5 + gsoc2022/smilesdb/data-catalog/jsconfig.json |19 + gsoc2022/smilesdb/data-catalog/package.json|51 + gsoc2022/smilesdb/data-catalog/public/favicon.ico | Bin 0 -> 4286 bytes gsoc2022/smilesdb/data-catalog/public/index.html |23 + gsoc2022/smilesdb/data-catalog/src/App.vue |30 + .../src/assets/data-catalog-overview.png | Bin 0 -> 464167 bytes gsoc2022/smilesdb/data-catalog/src/assets/logo.png | Bin 0 -> 6849 bytes .../data-catalog/src/components/AppHeader.vue |40 + .../data-catalog/src/components/CallBack.vue |47 + .../data-catalog/src/components/NavBar.vue |42 + gsoc2022/smilesdb/data-catalog/src/main.js |22 + .../data-catalog/src/pages/AccountInfo.vue |29 + .../smilesdb/data-catalog/src/pages/DataSheet.vue |17 + .../data-catalog/src/pages/DirectoryPage.vue |13 + .../smilesdb/data-catalog/src/pages/HomePage.vue |66 + .../smilesdb/data-catalog/src/pages/LoginPage.vue |95 + .../smilesdb/data-catalog/src/pages/SearchPage.vue | 194 + gsoc2022/smilesdb/data-catalog/src/router.js |45 + gsoc2022/smilesdb/data-catalog/vue.config.js |24 + gsoc2022/smilesdb/data-catalog/yarn.lock | 7079 +++ gsoc2022/smilesdb/rpc_handler/calc_info_pb2.py | 137 + .../smilesdb/rpc_handler/calc_info_pb2_grpc.py | 198 + .../smilesdb/rpc_handler/dataHandler}/__init__.py | 0 .../__pycache__/__init__.cpython-38.pyc| Bin 0 -> 169 bytes .../__pycache__/__init__.cpython-39.pyc| Bin 0 -> 169 bytes .../dataHandler/__pycache__/admin.cpython-38.pyc | Bin 0 -> 210 bytes .../dataHandler/__pycache__/admin.cpython-39.pyc | Bin 0 -> 210 bytes .../dataHandler/__pycache__/apps.cpython-38.pyc| Bin 0 -> 456 bytes .../dataHandler/__pycache__/apps.cpython-39.pyc| Bin 0 -> 456 bytes .../dataHandler/__pycache__/models.cpython-38.pyc | Bin 0 -> 207 bytes .../dataHandler/__pycache__/models.cpython-39.pyc | Bin 0 -> 207 bytes
[airavata-sandbox] 17/26: added stubs & code refactor
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 ec76f4c70c89367308f9dadfcb8251f543e1b47c
Author: Bhavesh Asanabada
AuthorDate: Mon Jul 25 11:25:12 2022 +0530
added stubs & code refactor
---
.../DjangoMiddleware/calc_properties_pb2.py| 56 +++
.../DjangoMiddleware/calc_properties_pb2_grpc.py | 165 +
.../smilesdb/DjangoMiddleware/calc_topology_pb2.py | 54 +++
.../DjangoMiddleware/calc_topology_pb2_grpc.py | 165 +
.../smilesdb/DjangoMiddleware/calcinfo/views.py| 9 +-
gsoc2022/smilesdb/DjangoMiddleware/molecule_pb2.py | 48 ++
.../smilesdb/DjangoMiddleware/molecule_pb2_grpc.py | 165 +
.../smilesdb/smiles_dashboard/public/favicon.ico | Bin 4286 -> 0 bytes
.../smiles_dashboard/src/components/HelloWorld.vue | 58
gsoc2022/smilesdb/smiles_dashboard/src/main.js | 7 +-
gsoc2022/smilesdb/smiles_dashboard/src/routers.js | 11 +-
11 files changed, 674 insertions(+), 64 deletions(-)
diff --git a/gsoc2022/smilesdb/DjangoMiddleware/calc_properties_pb2.py
b/gsoc2022/smilesdb/DjangoMiddleware/calc_properties_pb2.py
new file mode 100644
index ..3dfebd95
--- /dev/null
+++ b/gsoc2022/smilesdb/DjangoMiddleware/calc_properties_pb2.py
@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+# Generated by the protocol buffer compiler. DO NOT EDIT!
+# source: calc_properties.proto
+"""Generated protocol buffer code."""
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import descriptor_pool as _descriptor_pool
+from google.protobuf import message as _message
+from google.protobuf import reflection as _reflection
+from google.protobuf import symbol_database as _symbol_database
+# @@protoc_insertion_point(imports)
+
+_sym_db = _symbol_database.Default()
+
+
+
+
+DESCRIPTOR =
_descriptor_pool.Default().AddSerializedFile(b'\n\x15\x63\x61lc_properties.proto\x12\ncom.smiles\"\x95\x08\n\tCalcProps\x12\r\n\x05InChI\x18\x01
\x01(\t\x12\x10\n\x08InChIKey\x18\x02 \x01(\t\x12\x0e\n\x06SMILES\x18\x03
\x01(\t\x12\x17\n\x0f\x43\x61nonicalSMILES\x18\x04
\x01(\t\x12\x0b\n\x03PDB\x18\x05 \x01(\t\x12\x0b\n\x03SDF\x18\x06
\x01(\t\x12\x10\n\x08ParsedBy\x18\x07 \x01(\t\x12\x0f\n\x07\x46ormula\x18\x08
\x01(\t\x12\x0e\n\x06\x43harge\x18\t \x01(\x03\x12\x14\n\x0cMulti [...]
+
+
+
+_CALCPROPS = DESCRIPTOR.message_types_by_name['CalcProps']
+_CALCPROPSREQUEST = DESCRIPTOR.message_types_by_name['CalcPropsRequest']
+CalcProps = _reflection.GeneratedProtocolMessageType('CalcProps',
(_message.Message,), {
+ 'DESCRIPTOR' : _CALCPROPS,
+ '__module__' : 'calc_properties_pb2'
+ # @@protoc_insertion_point(class_scope:com.smiles.CalcProps)
+ })
+_sym_db.RegisterMessage(CalcProps)
+
+CalcPropsRequest =
_reflection.GeneratedProtocolMessageType('CalcPropsRequest',
(_message.Message,), {
+ 'DESCRIPTOR' : _CALCPROPSREQUEST,
+ '__module__' : 'calc_properties_pb2'
+ # @@protoc_insertion_point(class_scope:com.smiles.CalcPropsRequest)
+ })
+_sym_db.RegisterMessage(CalcPropsRequest)
+
+_CALCPROPSSERVICE = DESCRIPTOR.services_by_name['CalcPropsService']
+if _descriptor._USE_C_DESCRIPTORS == False:
+
+ DESCRIPTOR._options = None
+ DESCRIPTOR._serialized_options = b'P\001'
+ _CALCPROPS.fields_by_name['Homos']._options = None
+ _CALCPROPS.fields_by_name['Homos']._serialized_options = b'\020\001'
+ _CALCPROPS.fields_by_name['ScfEnergies']._options = None
+ _CALCPROPS.fields_by_name['ScfEnergies']._serialized_options = b'\020\001'
+ _CALCPROPS.fields_by_name['MoEnergies']._options = None
+ _CALCPROPS.fields_by_name['MoEnergies']._serialized_options = b'\020\001'
+ _CALCPROPS.fields_by_name['AtomCoords']._options = None
+ _CALCPROPS.fields_by_name['AtomCoords']._serialized_options = b'\020\001'
+ _CALCPROPS._serialized_start=38
+ _CALCPROPS._serialized_end=1083
+ _CALCPROPSREQUEST._serialized_start=1085
+ _CALCPROPSREQUEST._serialized_end=1168
+ _CALCPROPSSERVICE._serialized_start=1171
+ _CALCPROPSSERVICE._serialized_end=1482
+# @@protoc_insertion_point(module_scope)
diff --git a/gsoc2022/smilesdb/DjangoMiddleware/calc_properties_pb2_grpc.py
b/gsoc2022/smilesdb/DjangoMiddleware/calc_properties_pb2_grpc.py
new file mode 100644
index ..08a13ca0
--- /dev/null
+++ b/gsoc2022/smilesdb/DjangoMiddleware/calc_properties_pb2_grpc.py
@@ -0,0 +1,165 @@
+# Generated by the gRPC Python protocol compiler plugin. DO NOT EDIT!
+"""Client and server classes corresponding to protobuf-defined services."""
+import grpc
+
+import calc_properties_pb2 as calc__properties__pb2
+
+
+class CalcPropsServiceStub(object):
+"""Missing associated documentation comment in .proto file."""
+
+def __init__(self, channel):
+"""Constructor.
+
+Args:
+channel: A grpc.Channel.
+"""
+self.GetCalcProps = channel.unary_unary(
+
[airavata-sandbox] 02/26: Create README.md
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 e72236340897cb0d4ab4c30f8b12493ba1f3a77b Author: Bhavesh Asanabada <62237873+bhavesh-as...@users.noreply.github.com> AuthorDate: Mon Jun 27 08:08:58 2022 +0530 Create README.md --- gsoc2022/smilesdb/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/gsoc2022/smilesdb/README.md b/gsoc2022/smilesdb/README.md new file mode 100644 index ..165c960e --- /dev/null +++ b/gsoc2022/smilesdb/README.md @@ -0,0 +1 @@ +On Build!!
[airavata-sandbox] 23/26: added UI components
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 b602ddf3db45617c3468172957bc5c52a10a2339 Author: Bhavesh Asanabada AuthorDate: Mon Sep 12 13:44:23 2022 +0530 added UI components --- gsoc2022/smilesdb/data-catalog | 1 + 1 file changed, 1 insertion(+) diff --git a/gsoc2022/smilesdb/data-catalog b/gsoc2022/smilesdb/data-catalog new file mode 16 index ..0394951e --- /dev/null +++ b/gsoc2022/smilesdb/data-catalog @@ -0,0 +1 @@ +Subproject commit 0394951e6c2e3a178b1539165d20486eee0e20bd
[airavata-sandbox] 24/26: added the rpc streamline
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 76c6e42b3ad98501cb9bc2663c839e7494112c71 Author: Bhavesh Asanabada AuthorDate: Mon Sep 12 13:45:35 2022 +0530 added the rpc streamline --- gsoc2022/smilesdb/rpc_handler/calc_info_pb2.py | 137 ++ .../smilesdb/rpc_handler/calc_info_pb2_grpc.py | 198 + .../smilesdb/rpc_handler/dataHandler/__init__.py | 0 .../__pycache__/__init__.cpython-38.pyc| Bin 0 -> 169 bytes .../__pycache__/__init__.cpython-39.pyc| Bin 0 -> 169 bytes .../dataHandler/__pycache__/admin.cpython-38.pyc | Bin 0 -> 210 bytes .../dataHandler/__pycache__/admin.cpython-39.pyc | Bin 0 -> 210 bytes .../dataHandler/__pycache__/apps.cpython-38.pyc| Bin 0 -> 456 bytes .../dataHandler/__pycache__/apps.cpython-39.pyc| Bin 0 -> 456 bytes .../dataHandler/__pycache__/models.cpython-38.pyc | Bin 0 -> 207 bytes .../dataHandler/__pycache__/models.cpython-39.pyc | Bin 0 -> 207 bytes .../dataHandler/__pycache__/urls.cpython-38.pyc| Bin 0 -> 290 bytes .../dataHandler/__pycache__/urls.cpython-39.pyc| Bin 0 -> 290 bytes .../dataHandler/__pycache__/views.cpython-38.pyc | Bin 0 -> 2643 bytes .../dataHandler/__pycache__/views.cpython-39.pyc | Bin 0 -> 2655 bytes gsoc2022/smilesdb/rpc_handler/dataHandler/admin.py | 3 + gsoc2022/smilesdb/rpc_handler/dataHandler/apps.py | 6 + .../rpc_handler/dataHandler/code_gen/__init__.py | 0 .../code_gen/__pycache__/__init__.cpython-39.pyc | Bin 0 -> 178 bytes .../rpc_handler/dataHandler/migrations/__init__.py | 0 .../migrations/__pycache__/__init__.cpython-38.pyc | Bin 0 -> 180 bytes .../migrations/__pycache__/__init__.cpython-39.pyc | Bin 0 -> 180 bytes .../smilesdb/rpc_handler/dataHandler/models.py | 3 + .../rpc_handler/dataHandler/protos/calc_info.proto | 73 .../rpc_handler/dataHandler/protos/molecule.proto | 116 gsoc2022/smilesdb/rpc_handler/dataHandler/tests.py | 3 + gsoc2022/smilesdb/rpc_handler/dataHandler/urls.py | 7 + gsoc2022/smilesdb/rpc_handler/dataHandler/views.py | 128 + gsoc2022/smilesdb/rpc_handler/db.sqlite3 | 0 gsoc2022/smilesdb/rpc_handler/manage.py| 22 +++ gsoc2022/smilesdb/rpc_handler/molecule_pb2.py | 137 ++ gsoc2022/smilesdb/rpc_handler/molecule_pb2_grpc.py | 198 + gsoc2022/smilesdb/rpc_handler/requirements.txt | 12 ++ .../smilesdb/rpc_handler/rpc_handler/__init__.py | 0 .../__pycache__/__init__.cpython-38.pyc| Bin 0 -> 169 bytes .../__pycache__/__init__.cpython-39.pyc| Bin 0 -> 169 bytes .../__pycache__/settings.cpython-38.pyc| Bin 0 -> 2516 bytes .../__pycache__/settings.cpython-39.pyc| Bin 0 -> 2446 bytes .../rpc_handler/__pycache__/urls.cpython-38.pyc| Bin 0 -> 1006 bytes .../rpc_handler/__pycache__/urls.cpython-39.pyc| Bin 0 -> 1006 bytes .../rpc_handler/__pycache__/wsgi.cpython-38.pyc| Bin 0 -> 580 bytes .../rpc_handler/__pycache__/wsgi.cpython-39.pyc| Bin 0 -> 580 bytes gsoc2022/smilesdb/rpc_handler/rpc_handler/asgi.py | 16 ++ .../smilesdb/rpc_handler/rpc_handler/settings.py | 118 gsoc2022/smilesdb/rpc_handler/rpc_handler/urls.py | 24 +++ gsoc2022/smilesdb/rpc_handler/rpc_handler/wsgi.py | 16 ++ 46 files changed, 1217 insertions(+) diff --git a/gsoc2022/smilesdb/rpc_handler/calc_info_pb2.py b/gsoc2022/smilesdb/rpc_handler/calc_info_pb2.py new file mode 100644 index ..892bcfd3 --- /dev/null +++ b/gsoc2022/smilesdb/rpc_handler/calc_info_pb2.py @@ -0,0 +1,137 @@ +# -*- coding: utf-8 -*- +# Generated by the protocol buffer compiler. DO NOT EDIT! +# source: calc_info.proto +"""Generated protocol buffer code.""" +from google.protobuf import descriptor as _descriptor +from google.protobuf import descriptor_pool as _descriptor_pool +from google.protobuf import message as _message +from google.protobuf import reflection as _reflection +from google.protobuf import symbol_database as _symbol_database +# @@protoc_insertion_point(imports) + +_sym_db = _symbol_database.Default() + + + + +DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x0f\x63\x61lc_info.proto\x12\x08\x63\x61lcInfo\"\x8a\x01\n\x08\x43\x61lcInfo\x12\x13\n\x0b\x63\x61lcinfo_id\x18\x01 \x01(\t\x12\x0e\n\x06smiles\x18\x02 \x01(\t\x12\x0e\n\x06nbasis\x18\x03 \x01(\x03\x12\x0b\n\x03nmo\x18\x04 \x01(\x03\x12\x0e\n\x06nalpha\x18\x05 \x01(\x03\x12\r\n\x05nbeta\x18\x06 \x01(\x03\x12\r\n\x05natom\x18\x07 \x01(\x03\x12\x0e\n\x06\x65nergy\x18\x08 \x01(\x01\"9\n\x11\x43reateInfoRequest\x12$\n\x08\x63\x61 [...] + + + +_CALCINFO = DESCRIPTOR.message_types_by_name['CalcInfo'] +_CREATEINFOREQUEST = DESCRIPTOR.message_types_by_name['CreateInfoRequest'] +_CREATEINFORESPONSE =
[airavata-sandbox] 01/26: Query SMILES Data
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 0fb564587eb7dfd61c480a46129e5330f5c4bb7d Author: Bhavesh Asanabada AuthorDate: Mon Jun 27 08:04:08 2022 +0530 Query SMILES Data --- gsoc2022/smilesdb/README | 1 - gsoc2022/smilesdb/Server/.gitignore| 33 + gsoc2022/smilesdb/Server/mvnw | 316 + gsoc2022/smilesdb/Server/mvnw.cmd | 188 + .../main/java/com/smiles/ServerApplication.java| 24 + .../src/main/java/com/smiles/SpringContext.java| 21 + .../java/com/smiles/calcinfo/CalcInfoEntity.java | 94 +++ .../java/com/smiles/calcinfo/CalcInfoImpl.java | 91 +++ .../java/com/smiles/calcinfo/CalcInfoRepo.java | 13 + .../java/com/smiles/calcprops/CalcPropsEntity.java | 616 + .../java/com/smiles/calcprops/CalcPropsImpl.java | 149 .../java/com/smiles/calcprops/CalcPropsRepo.java | 8 + .../smiles/calctopology/CalcTopologyEntity.java| 123 .../com/smiles/calctopology/CalcTopologyImpl.java | 52 ++ .../com/smiles/calctopology/CalcTopologyRepo.java | 10 + .../java/com/smiles/molData/MoleculeEntity.java| 761 + .../main/java/com/smiles/molData/MoleculeImpl.java | 97 +++ .../main/java/com/smiles/molData/MoleculeRepo.java | 8 + .../smilesdb/Server/src/main/proto/calc_info.proto | 49 ++ .../Server/src/main/proto/calc_properties.proto| 117 .../Server/src/main/proto/calc_topology.proto | 53 ++ .../smilesdb/Server/src/main/proto/molecule.proto | 119 .../src/main/resources/application.properties | 2 + .../java/com/smiles/ServerApplicationTests.java| 13 + .../__pycache__/calc_info_pb2.cpython-38.pyc | Bin 0 -> 1629 bytes .../__pycache__/calc_info_pb2_grpc.cpython-38.pyc | Bin 0 -> 4098 bytes gsoc2022/smilesdb/smiles_client/calc_info_pb2.py | 47 ++ .../smilesdb/smiles_client/calc_info_pb2_grpc.py | 165 + gsoc2022/smilesdb/smiles_client/main.py| 56 ++ .../smilesdb/smiles_client/proto/calc_info.proto | 40 ++ 30 files changed, 3265 insertions(+), 1 deletion(-) diff --git a/gsoc2022/smilesdb/README b/gsoc2022/smilesdb/README deleted file mode 100644 index 4ea7287d.. --- a/gsoc2022/smilesdb/README +++ /dev/null @@ -1 +0,0 @@ -GSoC project to create databases for smiles diff --git a/gsoc2022/smilesdb/Server/.gitignore b/gsoc2022/smilesdb/Server/.gitignore new file mode 100644 index ..549e00a2 --- /dev/null +++ b/gsoc2022/smilesdb/Server/.gitignore @@ -0,0 +1,33 @@ +HELP.md +target/ +!.mvn/wrapper/maven-wrapper.jar +!**/src/main/**/target/ +!**/src/test/**/target/ + +### STS ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache + +### IntelliJ IDEA ### +.idea +*.iws +*.iml +*.ipr + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ +build/ +!**/src/main/**/build/ +!**/src/test/**/build/ + +### VS Code ### +.vscode/ diff --git a/gsoc2022/smilesdb/Server/mvnw b/gsoc2022/smilesdb/Server/mvnw new file mode 100755 index ..8a8fb228 --- /dev/null +++ b/gsoc2022/smilesdb/Server/mvnw @@ -0,0 +1,316 @@ +#!/bin/sh +# +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +#https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +# + +# +# Maven Start Up Batch script +# +# Required ENV vars: +# -- +# JAVA_HOME - location of a JDK home dir +# +# Optional ENV vars +# - +# M2_HOME - location of maven2's installed home dir +# MAVEN_OPTS - parameters passed to the Java VM when running Maven +# e.g. to debug Maven itself, use +# set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000 +# MAVEN_SKIP_RC - flag to disable loading of mavenrc files +# + +if [ -z "$MAVEN_SKIP_RC" ] ; then + + if [
[airavata-sandbox] 07/26: refactor client
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 3174daebd5f8f93f4f33efacf498018cf0835607
Author: Bhavesh Asanabada
AuthorDate: Mon Jul 4 06:20:34 2022 +0530
refactor client
---
.../__pycache__/calc_info_pb2.cpython-38.pyc | Bin 1629 -> 0 bytes
.../__pycache__/calc_info_pb2_grpc.cpython-38.pyc | Bin 4098 -> 0 bytes
gsoc2022/smilesdb/smiles_client/calc_info_pb2.py | 47 --
.../smilesdb/smiles_client/calc_info_pb2_grpc.py | 165 -
gsoc2022/smilesdb/smiles_client/main.py| 56 ---
.../smilesdb/smiles_client/proto/calc_info.proto | 40 -
6 files changed, 308 deletions(-)
diff --git
a/gsoc2022/smilesdb/smiles_client/__pycache__/calc_info_pb2.cpython-38.pyc
b/gsoc2022/smilesdb/smiles_client/__pycache__/calc_info_pb2.cpython-38.pyc
deleted file mode 100644
index 7d70f051..
Binary files
a/gsoc2022/smilesdb/smiles_client/__pycache__/calc_info_pb2.cpython-38.pyc and
/dev/null differ
diff --git
a/gsoc2022/smilesdb/smiles_client/__pycache__/calc_info_pb2_grpc.cpython-38.pyc
b/gsoc2022/smilesdb/smiles_client/__pycache__/calc_info_pb2_grpc.cpython-38.pyc
deleted file mode 100644
index 3776d2a0..
Binary files
a/gsoc2022/smilesdb/smiles_client/__pycache__/calc_info_pb2_grpc.cpython-38.pyc
and /dev/null differ
diff --git a/gsoc2022/smilesdb/smiles_client/calc_info_pb2.py
b/gsoc2022/smilesdb/smiles_client/calc_info_pb2.py
deleted file mode 100644
index 37a1074a..
--- a/gsoc2022/smilesdb/smiles_client/calc_info_pb2.py
+++ /dev/null
@@ -1,47 +0,0 @@
-# -*- coding: utf-8 -*-
-# Generated by the protocol buffer compiler. DO NOT EDIT!
-# source: calc_info.proto
-"""Generated protocol buffer code."""
-from google.protobuf import descriptor as _descriptor
-from google.protobuf import descriptor_pool as _descriptor_pool
-from google.protobuf import message as _message
-from google.protobuf import reflection as _reflection
-from google.protobuf import symbol_database as _symbol_database
-# @@protoc_insertion_point(imports)
-
-_sym_db = _symbol_database.Default()
-
-
-
-
-DESCRIPTOR =
_descriptor_pool.Default().AddSerializedFile(b'\n\x0f\x63\x61lc_info.proto\x12\ncom.smiles\"u\n\x08\x43\x61lcInfo\x12\x0e\n\x06nbasis\x18\x01
\x01(\x03\x12\x0b\n\x03nmo\x18\x02 \x01(\x03\x12\x0e\n\x06nalpha\x18\x03
\x01(\x03\x12\r\n\x05nbeta\x18\x04 \x01(\x03\x12\r\n\x05natom\x18\x05
\x01(\x03\x12\x0e\n\x06\x65nergy\x18\x06 \x01(\x01\x12\x0e\n\x06SMILES\x18\x07
\x01(\t\"P\n\x0f\x43\x61lcInfoRequest\x12\x15\n\rcalcInfoQuery\x18\x01
\x01(\t\x12&\n\x08\x63\x61lcInfo\x18\x02 \x0 [...]
-
-
-
-_CALCINFO = DESCRIPTOR.message_types_by_name['CalcInfo']
-_CALCINFOREQUEST = DESCRIPTOR.message_types_by_name['CalcInfoRequest']
-CalcInfo = _reflection.GeneratedProtocolMessageType('CalcInfo',
(_message.Message,), {
- 'DESCRIPTOR' : _CALCINFO,
- '__module__' : 'calc_info_pb2'
- # @@protoc_insertion_point(class_scope:com.smiles.CalcInfo)
- })
-_sym_db.RegisterMessage(CalcInfo)
-
-CalcInfoRequest = _reflection.GeneratedProtocolMessageType('CalcInfoRequest',
(_message.Message,), {
- 'DESCRIPTOR' : _CALCINFOREQUEST,
- '__module__' : 'calc_info_pb2'
- # @@protoc_insertion_point(class_scope:com.smiles.CalcInfoRequest)
- })
-_sym_db.RegisterMessage(CalcInfoRequest)
-
-_CALCINFOSERVICE = DESCRIPTOR.services_by_name['CalcInfoService']
-if _descriptor._USE_C_DESCRIPTORS == False:
-
- DESCRIPTOR._options = None
- _CALCINFO._serialized_start=31
- _CALCINFO._serialized_end=148
- _CALCINFOREQUEST._serialized_start=150
- _CALCINFOREQUEST._serialized_end=230
- _CALCINFOSERVICE._serialized_start=233
- _CALCINFOSERVICE._serialized_end=531
-# @@protoc_insertion_point(module_scope)
diff --git a/gsoc2022/smilesdb/smiles_client/calc_info_pb2_grpc.py
b/gsoc2022/smilesdb/smiles_client/calc_info_pb2_grpc.py
deleted file mode 100644
index dcb4a1b5..
--- a/gsoc2022/smilesdb/smiles_client/calc_info_pb2_grpc.py
+++ /dev/null
@@ -1,165 +0,0 @@
-# Generated by the gRPC Python protocol compiler plugin. DO NOT EDIT!
-"""Client and server classes corresponding to protobuf-defined services."""
-import grpc
-
-import calc_info_pb2 as calc__info__pb2
-
-
-class CalcInfoServiceStub(object):
-"""Missing associated documentation comment in .proto file."""
-
-def __init__(self, channel):
-"""Constructor.
-
-Args:
-channel: A grpc.Channel.
-"""
-self.GetCalcInfo = channel.unary_unary(
-'/com.smiles.CalcInfoService/GetCalcInfo',
-
request_serializer=calc__info__pb2.CalcInfoRequest.SerializeToString,
-response_deserializer=calc__info__pb2.CalcInfo.FromString,
-)
-self.CreateCalcInfo = channel.unary_unary(
-'/com.smiles.CalcInfoService/CreateCalcInfo',
-
[airavata-sandbox] 08/26: added pom file
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 bda01d7d23c53795e198e5efbf57303124a954ae
Author: Bhavesh Asanabada
AuthorDate: Thu Jul 14 18:31:16 2022 +0530
added pom file
---
gsoc2022/smilesdb/Server/pom.xml | 91
1 file changed, 91 insertions(+)
diff --git a/gsoc2022/smilesdb/Server/pom.xml b/gsoc2022/smilesdb/Server/pom.xml
new file mode 100644
index ..cdf8e940
--- /dev/null
+++ b/gsoc2022/smilesdb/Server/pom.xml
@@ -0,0 +1,91 @@
+
+http://maven.apache.org/POM/4.0.0;
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance;
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
https://maven.apache.org/xsd/maven-4.0.0.xsd;>
+4.0.0
+
+org.springframework.boot
+spring-boot-starter-parent
+2.7.0
+
+
+com.smiles
+Server
+0.0.1-SNAPSHOT
+Server
+Server
+
+18
+
+
+
+org.springframework.boot
+spring-boot-starter
+
+
+org.springframework.boot
+spring-boot-starter-test
+test
+
+
+org.springframework.boot
+spring-boot-starter-data-mongodb
+
+
+io.grpc
+grpc-netty-shaded
+1.47.0
+runtime
+
+
+io.grpc
+grpc-protobuf
+1.47.0
+
+
+io.grpc
+grpc-stub
+1.47.0
+
+
+org.apache.tomcat
+annotations-api
+6.0.53
+provided
+
+
+
+
+
+
+kr.motd.maven
+os-maven-plugin
+1.6.2
+
+
+
+
+org.springframework.boot
+spring-boot-maven-plugin
+
+
+org.xolstice.maven.plugins
+protobuf-maven-plugin
+0.6.1
+
+
com.google.protobuf:protoc:3.19.2:exe:${os.detected.classifier}
+grpc-java
+
io.grpc:protoc-gen-grpc-java:1.47.0:exe:${os.detected.classifier}
+
+
+
+
+compile
+compile-custom
+
+
+
+
+
+
+
+
[airavata-sandbox] 03/26: Added CRUD methods to MolData
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 b1320cef005d06cb8bd44a2892023dab8d86ec6b
Author: Bhavesh Asanabada
AuthorDate: Mon Jun 27 14:16:25 2022 +0530
Added CRUD methods to MolData
---
.../java/com/smiles/calcinfo/CalcInfoImpl.java | 2 -
.../java/com/smiles/calcinfo/CalcInfoRepo.java | 2 +-
.../java/com/smiles/calcprops/CalcPropsEntity.java | 2 +
.../java/com/smiles/calcprops/CalcPropsImpl.java | 15 ++--
.../java/com/smiles/calcprops/CalcPropsRepo.java | 4 +-
.../com/smiles/calctopology/CalcTopologyImpl.java | 4 +-
.../main/java/com/smiles/molData/MoleculeImpl.java | 82 +-
7 files changed, 98 insertions(+), 13 deletions(-)
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java
index 3798ca5e..221bf9cc 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoImpl.java
@@ -77,7 +77,6 @@ public class CalcInfoImpl extends
CalcInfoServiceGrpc.CalcInfoServiceImplBase {
responseObserver.onCompleted();
}
-
@Override
public void deleteCalcInfo(com.smiles.CalcInfoRequest request,
io.grpc.stub.StreamObserver responseObserver) {
@@ -87,5 +86,4 @@ public class CalcInfoImpl extends
CalcInfoServiceGrpc.CalcInfoServiceImplBase {
responseObserver.onNext(calcInfo);
responseObserver.onCompleted();
}
-
}
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoRepo.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoRepo.java
index 37611c92..2abe1fb0 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoRepo.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcinfo/CalcInfoRepo.java
@@ -4,7 +4,7 @@ import
org.springframework.data.mongodb.repository.MongoRepository;
public interface CalcInfoRepo extends MongoRepository {
-public CalcInfoEntity findByNalpha(long nalpha);
+//public CalcInfoEntity findByNalpha(long nalpha);
public CalcInfoEntity findBySMILES(String SMILES);
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsEntity.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsEntity.java
index e9b495c3..dbcbb1bd 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsEntity.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsEntity.java
@@ -1,11 +1,13 @@
package com.smiles.calcprops;
import org.springframework.data.annotation.Id;
+import org.springframework.data.mongodb.core.mapping.Document;
import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.List;
+@Document("calcProps")
public class CalcPropsEntity {
@Id
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsImpl.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsImpl.java
index 3aec2474..47ca39c7 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsImpl.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calcprops/CalcPropsImpl.java
@@ -15,8 +15,8 @@ public class CalcPropsImpl extends
CalcPropsServiceGrpc.CalcPropsServiceImplBase
public void getCalcProps(CalcPropsRequest request,
StreamObserver responseObserver) {
//super.getCalcInfo(request, responseObserver);
-CalcPropsEntity calcProps =
repo1.findByPDB(request.getCalcPropsQuery());
-System.out.println(calcProps);
+CalcPropsEntity calcProps =
repo1.findBySMILES(request.getCalcPropsQuery());
+System.out.println(calcProps.toString());
CalcProps reply = CalcProps.newBuilder()
.setInChI(calcProps.getInChI())
@@ -69,7 +69,9 @@ public class CalcPropsImpl extends
CalcPropsServiceGrpc.CalcPropsServiceImplBase
calcProps.getOtherinfo(), calcProps.getComments(),
calcProps.getNAtom(),
calcProps.getHomosList(), calcProps.getScfEnergiesList(),
calcProps.getMoEnergiesList(),
calcProps.getAtomCoordsList(), calcProps.getNmo(),
calcProps.getNBasis());
-
+repo1.save(c2001);
+responseObserver.onNext(calcProps);
+responseObserver.onCompleted();
}
@Override
@@ -77,7 +79,7 @@ public class CalcPropsImpl extends
CalcPropsServiceGrpc.CalcPropsServiceImplBase
//super.updateCalcProps(request, responseObserver);
CalcProps calcProps = request.getCalcProp();
System.out.println(request.getAllFields());
-CalcPropsEntity c2001 = (CalcPropsEntity)
repo1.findByPDB(calcProps.getPDB());
+
[airavata-sandbox] 11/26: Added router view
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 a26cda1769902b8029cfa2b47cc74bc77bd851c5
Author: Bhavesh Asanabada
AuthorDate: Thu Jul 14 22:30:04 2022 +0530
Added router view
---
gsoc2022/smilesdb/smiles_dashboard/src/App.vue| 23 ++--
gsoc2022/smilesdb/smiles_dashboard/src/main.js| 4 +++-
gsoc2022/smilesdb/smiles_dashboard/src/routers.js | 26 +++
3 files changed, 36 insertions(+), 17 deletions(-)
diff --git a/gsoc2022/smilesdb/smiles_dashboard/src/App.vue
b/gsoc2022/smilesdb/smiles_dashboard/src/App.vue
index 98060536..41a32c3d 100644
--- a/gsoc2022/smilesdb/smiles_dashboard/src/App.vue
+++ b/gsoc2022/smilesdb/smiles_dashboard/src/App.vue
@@ -1,35 +1,26 @@
-
-
-
+
-// import HelloWorld from './components/HelloWorld.vue'
-//
-// export default {
-// name: 'App',
-// components: {
-// HelloWorld
-// }
-import CalcInfo from './components/CalcInfo.vue'
export default {
name: 'App',
- components: {
-CalcInfo,
- }
}
+*{
+ margin: 0;
+ padding: 0;
+}
#app {
- font-family: Avenir, Helvetica, Arial, sans-serif;
+ font-family: "Times New Roman",sans-serif;
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
text-align: center;
color: #2c3e50;
- margin-top: 60px;
+ margin-top: 0px;
}
diff --git a/gsoc2022/smilesdb/smiles_dashboard/src/main.js
b/gsoc2022/smilesdb/smiles_dashboard/src/main.js
index 01433bca..c982a778 100644
--- a/gsoc2022/smilesdb/smiles_dashboard/src/main.js
+++ b/gsoc2022/smilesdb/smiles_dashboard/src/main.js
@@ -1,4 +1,6 @@
import { createApp } from 'vue'
import App from './App.vue'
-createApp(App).mount('#app')
+import router from "./routers"
+
+createApp(App).use(router).mount('#app')
diff --git a/gsoc2022/smilesdb/smiles_dashboard/src/routers.js
b/gsoc2022/smilesdb/smiles_dashboard/src/routers.js
new file mode 100644
index ..95358f32
--- /dev/null
+++ b/gsoc2022/smilesdb/smiles_dashboard/src/routers.js
@@ -0,0 +1,26 @@
+import LoginPage from "./components/LoginPage";
+import CalcInfo from "./components/CalcInfo";
+
+import {createRouter, createWebHistory} from 'vue-router';
+
+const routes = [
+{
+name: 'Home',
+component: LoginPage,
+path:'/'
+},
+{
+name: 'CalcInfo',
+component: CalcInfo,
+path:'/calcinfo'
+}
+];
+
+const router = createRouter(
+{
+history:createWebHistory(),
+routes
+}
+)
+
+export default router
\ No newline at end of file
[airavata-sandbox] 04/26: Resolved issues in calc_topology builder
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 451792418d020430d32d735a55d04e40c14d2401
Author: Bhavesh Asanabada
AuthorDate: Tue Jun 28 12:03:12 2022 +0530
Resolved issues in calc_topology builder
---
.../com/smiles/calctopology/CalcTopologyImpl.java | 18 ++-
.../com/smiles/calctopology/CalcTopologyRepo.java | 1 +
.../main/java/com/smiles/molData/MoleculeImpl.java | 146 ++---
.../Server/src/main/proto/calc_topology.proto | 6 +-
4 files changed, 88 insertions(+), 83 deletions(-)
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyImpl.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyImpl.java
index 2b143010..22fa6ec2 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyImpl.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyImpl.java
@@ -7,6 +7,7 @@ import com.smiles.SpringContext;
import io.grpc.stub.StreamObserver;
import javax.swing.*;
+import java.util.ArrayList;
public class CalcTopologyImpl extends
CalcTopologyServiceGrpc.CalcTopologyServiceImplBase {
@@ -16,20 +17,23 @@ public class CalcTopologyImpl extends
CalcTopologyServiceGrpc.CalcTopologyServic
//super.getCalcTopology(request, responseObserver);
System.out.println(request.getAllFields());
-CalcTopologyEntity calcTopology =
repo.findBySymbols(request.getcalcTopologyQuery());
+ArrayList input = new ArrayList();
+input.add(request.getCalcTopologyQuery());
+CalcTopologyEntity calcTopology = repo.findBySymbols(input);
System.out.println(calcTopology.toString());
CalcTopology reply = CalcTopology.newBuilder()
-.setSymbols(calcTopology.getSymbols())
-.setGeometry(calcTopology.getGeometry())
+.addAllSymbols(calcTopology.getSymbols())
+.addAllGeometry(calcTopology.getGeometry())
.setMolCharge(calcTopology.getMol_charge())
.setMolMultiplicity(calcTopology.getMol_multiplicity())
.setName(calcTopology.getName())
.setComment(calcTopology.getComment())
-.setMassNumbers(calcTopology.getMass_numbers())
-.setMasses(calcTopology.getMasses())
-.setAtomicNumber(calcTopology.getAtomic_number())
-.setAtomLabels(calcTopology.getAtomic_labels()).build();
+.addAllMassNumbers(calcTopology.getMass_numbers())
+.addAllMasses(calcTopology.getMasses())
+.addAllAtomicNumber(calcTopology.getAtomic_number())
+.addAllAtomLabels(calcTopology.getAtomic_labels()).build();
+
}
@Override
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyRepo.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyRepo.java
index a4fd1b98..2efbebea 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyRepo.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/calctopology/CalcTopologyRepo.java
@@ -7,4 +7,5 @@ import java.util.List;
public interface CalcTopologyRepo extends MongoRepository {
public CalcTopologyEntity findBySymbols(List symbols);
+
}
diff --git
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/molData/MoleculeImpl.java
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/molData/MoleculeImpl.java
index 6cf4a7b5..1b961a1a 100644
---
a/gsoc2022/smilesdb/Server/src/main/java/com/smiles/molData/MoleculeImpl.java
+++
b/gsoc2022/smilesdb/Server/src/main/java/com/smiles/molData/MoleculeImpl.java
@@ -55,7 +55,7 @@ public class MoleculeImpl extends
MoleculeServiceGrpc.MoleculeServiceImplBase {
//super.createMolecule(request, responseObserver);
Molecule molecule = request.getMolecule();
System.out.println(request.getAllFields());
-MoleculeEntity c4001 = new MoleculeEntity(molecule.getCasNr(),
+MoleculeEntity moleculeEntity = new MoleculeEntity(molecule.getCasNr(),
molecule.getSmiles(), molecule.getSmilesStereo(),
molecule.getInchi(), molecule.getMolfileBlobSource(),
molecule.getEmpFormula(), molecule.getEmpFormulaSort(),
@@ -78,7 +78,7 @@ public class MoleculeImpl extends
MoleculeServiceGrpc.MoleculeServiceImplBase {
molecule.getBpSource(), molecule.getSafetyR(),
molecule.getSafetyH(), molecule.getSafetyS(),
molecule.getSafetyP(), molecule.getSafetyText(),
molecule.getSafetySym(),
molecule.getSafetySymGhs(), molecule.getSafetySource(),
molecule.getCommentMol());
-repo.save(c4001);
+repo.save(moleculeEntity);
[airavata-sandbox] 09/26: created login page
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 4c550149add1057f4c15b28135df2891bdde5b6a
Author: Bhavesh Asanabada
AuthorDate: Thu Jul 14 22:25:25 2022 +0530
created login page
---
.../smiles_dashboard/src/assets/molecule_bg1.jpeg | Bin 0 -> 852281 bytes
.../smiles_dashboard/src/components/LoginPage.vue | 115 +
2 files changed, 115 insertions(+)
diff --git a/gsoc2022/smilesdb/smiles_dashboard/src/assets/molecule_bg1.jpeg
b/gsoc2022/smilesdb/smiles_dashboard/src/assets/molecule_bg1.jpeg
new file mode 100644
index ..b4aecb92
Binary files /dev/null and
b/gsoc2022/smilesdb/smiles_dashboard/src/assets/molecule_bg1.jpeg differ
diff --git a/gsoc2022/smilesdb/smiles_dashboard/src/components/LoginPage.vue
b/gsoc2022/smilesdb/smiles_dashboard/src/components/LoginPage.vue
new file mode 100644
index ..e96306c0
--- /dev/null
+++ b/gsoc2022/smilesdb/smiles_dashboard/src/components/LoginPage.vue
@@ -0,0 +1,115 @@
+
+
+Login Page
+
+
+
+
+SIGN IN
+Username
+
+Password
+
+Sign in
+Forgot Password?
+Login with CILogon
+
+
+
+
+
+
+
+export default {
+ name: "LoginPage"
+}
+
+
+
+* {
+ margin: 0;
+ padding: 0;
+ box-sizing: border-box;
+ font-family: 'Poppins', sans-serif;
+ cursor: pointer;
+}
+
+/*@import
url(https://fonts.googleapis.com/css2?family=Source+Sans+Pro&display=swap);*/
+
+body {
+ height: 100vh;
+ width: 100%;
+ display: flex;
+ justify-content: center;
+ align-items: center;
+ /*background: linear-gradient(to right, #2C2C2C, #2c3e50);*/
+ background-image: url("../assets/molecule_bg1.jpeg");
+}
+
+form {
+ width: 25rem;
+ height: 28rem;
+ margin-right: 50rem;
+ display: flex;
+ flex-direction: column;
+ background: rgba(255, 255, 255, 0.04);
+ box-shadow: 0 8px 32px 0 rgba(52, 52, 52, 0.52);
+ border-radius: 30px;
+ border-left: 1px solid rgba(255, 255, 255, 0.3);
+ border-top: 1px solid rgba(255, 255, 255, 0.3);
+ border-right: 1px solid rgba(255, 255, 255, 0.3);
+ border-bottom: 1px solid rgba(255, 255, 255, 0.3);
+}
+
+h1 {
+ font-size: 50px;
+ color: #edf0f1;
+ text-align: center;
+ text-shadow: 2px 2px 4px rgba(255, 255, 255, 0.3);
+ letter-spacing: 3px;
+ margin-top: 20px;
+ margin-bottom: 5%;
+ opacity: 0.7;
+}
+
+label {
+ font-size: 20px;
+ color: #edf0f1;
+ display: flex;
+ text-align: left;
+ margin-left: 10%;
+ margin-bottom:1px;
+ opacity: 0.8;
+ text-shadow: 2px 2px 4px rgba(255, 255, 255, 0.3);
+}
+
+input {
+ width: 80%;
+ height: 20px;
+ font-size: 18px;
+ margin: 5% auto 8%;
+ border: none;
+ outline: none;
+ background: transparent;
+ color: white;
+ border-bottom: 1px solid rgba(255, 255, 255, 0.6);
+}
+
+button {
+ width: 50%;
+ margin: 3% auto;
+ color: white;
+ font-size: 15px;
+ opacity: 0.7;
+ background: rgba(255, 255, 255, 0.06);
+ padding: 10px 30px;
+ border: none;
+ outline: none;
+ border-radius: 20px;
+ text-shadow: 2px 2px 4px rgba(255, 255, 255, 0.3);
+ box-shadow: 3px 3px 5px rgba(255, 255, 255, 0.32);
+ border-left: 2px solid rgba(255, 255, 255, 0.3);
+ border-right: 2px solid rgba(255, 255, 255, 0.3);
+ border-top: 2px solid rgba(255, 255, 255, 0.3);
+}
+
\ No newline at end of file
[airavata-sandbox] 10/26: created SEAGrid home page
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 224764ba5dc19518aacd7e2ba9c131fc165865e7
Author: Bhavesh Asanabada
AuthorDate: Thu Jul 14 22:26:26 2022 +0530
created SEAGrid home page
---
.../smiles_dashboard/src/components/SEAGrid.vue| 49 ++
1 file changed, 49 insertions(+)
diff --git a/gsoc2022/smilesdb/smiles_dashboard/src/components/SEAGrid.vue
b/gsoc2022/smilesdb/smiles_dashboard/src/components/SEAGrid.vue
new file mode 100644
index ..af7f29cb
--- /dev/null
+++ b/gsoc2022/smilesdb/smiles_dashboard/src/components/SEAGrid.vue
@@ -0,0 +1,49 @@
+
+
+Welcome to SEAGrid Data Catalog
+SEAGrid Data Catalog provides a sleek web interface for you to browse
and
+ search through your SEAGrid data. Currently the system can index outputs
of
+ several computational chemistry applications including Gaussian, Gamess,
+ Molpro and NWChem. Also it allows to publish your data into research data
+ publishing systems, do browser based visualization of molecular structure
+ and properties and to run complex search queries to filter the data.
+ So now you don't need to download all the data into your local machine
after
+ running a HPC application but select only the interesting data based on
the
+ results of configured post processing steps in the system.
+
+
+
+
+
+export default {
+ name: "SEAGrid"
+}
+
+
+
+
+ .container{
+width: 70em;
+height: 80em;
+margin-left: auto;
+margin-right: auto;
+ }
+ h1 {
+padding-top: 1em;
+position: center;
+text-decoration: black;
+ }
+ p{
+display: block;
+margin-block-start: 1em;
+margin-block-end: 1em;
+margin-inline-start: 0px;
+margin-inline-end: 0px;
+text-align: justify ;
+font-size: 21px;
+ }
+ .sys-architect{
+height: 500px;
+width: 700px;
+ }
+
\ No newline at end of file
[airavata-data-lake] branch master updated: Fixing shared_by
This is an automated email from the ASF dual-hosted git repository.
isjarana pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata-data-lake.git
The following commit(s) were added to refs/heads/master by this push:
new a4f3032 Fixing shared_by
new d8e2050 Merge pull request #168 from isururanawaka/mysql_conversion
a4f3032 is described below
commit a4f30328653dac64c0fa36050d420fa60715cb67
Author: Isuru Ranawaka
AuthorDate: Mon Sep 12 11:09:08 2022 -0400
Fixing shared_by
---
.../org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git
a/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
b/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
index 89e6c2f..c0a7f60 100644
---
a/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
+++
b/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
@@ -287,7 +287,7 @@ public class ResourceServiceHandler extends
ResourceServiceGrpc.ResourceServiceI
if(searchQuery.getField().equalsIgnoreCase("sharedBy")) {
SearchCriteria searchCriteria = SearchCriteria.newBuilder()
.setSearchField(EntitySearchField.SHARED_BY)
-
.setCondition(SearchCondition.valueOf(searchQuery.getOptions()))
+.setCondition(SearchCondition.EQUAL)
.setValue(searchQuery.getValue()).build();
searchRequestBuilder =
searchRequestBuilder.addSearchCriteria(searchCriteria);
[airavata-data-lake] branch master updated: Fixing shared_by
This is an automated email from the ASF dual-hosted git repository.
isjarana pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata-data-lake.git
The following commit(s) were added to refs/heads/master by this push:
new ae10895 Fixing shared_by
new d8bd857 Merge pull request #167 from isururanawaka/mysql_conversion
ae10895 is described below
commit ae10895a4097fb19de018cbef5d45c1301318930
Author: Isuru Ranawaka
AuthorDate: Mon Sep 12 11:00:49 2022 -0400
Fixing shared_by
---
.../org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git
a/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
b/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
index ef3b1e4..89e6c2f 100644
---
a/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
+++
b/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
@@ -284,9 +284,9 @@ public class ResourceServiceHandler extends
ResourceServiceGrpc.ResourceServiceI
for (ResourceSearchQuery searchQuery : resourceSearchQueries) {
-if(!searchQuery.getField().equals("shared_with")) {
+if(searchQuery.getField().equalsIgnoreCase("sharedBy")) {
SearchCriteria searchCriteria = SearchCriteria.newBuilder()
-
.setSearchField(EntitySearchField.valueOf(searchQuery.getField()))
+.setSearchField(EntitySearchField.SHARED_BY)
.setCondition(SearchCondition.valueOf(searchQuery.getOptions()))
.setValue(searchQuery.getValue()).build();
[airavata-sandbox] branch dependabot/npm_and_yarn/gsoc2022/jupyter-platform-dashboard/moment-2.29.4 created (now 2d2d2214)
This is an automated email from the ASF dual-hosted git repository. github-bot pushed a change to branch dependabot/npm_and_yarn/gsoc2022/jupyter-platform-dashboard/moment-2.29.4 in repository https://gitbox.apache.org/repos/asf/airavata-sandbox.git at 2d2d2214 Bump moment in /gsoc2022/jupyter-platform-dashboard No new revisions were added by this update.
[airavata-sandbox] 06/13: Update README.md
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 daf1b350c2b109e9f3e6bbc838cf4e627196e0bf Author: Aishwarya Vijay Sinhasane <48974593+aishwaryasinhas...@users.noreply.github.com> AuthorDate: Thu Jul 21 03:10:43 2022 -0400 Update README.md --- gsoc2022/seagrid-rich-client/README.md | 15 +++ 1 file changed, 15 insertions(+) diff --git a/gsoc2022/seagrid-rich-client/README.md b/gsoc2022/seagrid-rich-client/README.md index 72b651da..4cd99781 100644 --- a/gsoc2022/seagrid-rich-client/README.md +++ b/gsoc2022/seagrid-rich-client/README.md @@ -7,6 +7,21 @@ .png) ## Steps to Run the Application +### Installation Steps: + + To run electronJS application you need to install node.js. + Follow below installation steps for node.js + + - https://nodejs.org/en/download/ + + Check node.js installed + - npm -v + - node -v + + Now to install electronJS run below command. +- npm install --save-dev electron + + Run Application 1. Clone the repository. 2. Run below command - npm start
[airavata-sandbox] 13/13: README file updated
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 acb0eb95dc6bbc2fd84e38fbf5e19e262193ed35
Author: BECOB257_Aishwarya Sinhasane
AuthorDate: Sun Sep 11 20:56:49 2022 -0400
README file updated
---
.../{ => Images}/Modified_SeaGrid_Overview (2).png | Bin
gsoc2022/seagrid-rich-client/Images/Mol3dEditor.png | Bin 0 -> 246813 bytes
gsoc2022/seagrid-rich-client/Images/jsme.png | Bin 0 -> 199966 bytes
gsoc2022/seagrid-rich-client/Images/nglviewer.png| Bin 0 -> 334069 bytes
gsoc2022/seagrid-rich-client/README.md | 19 +--
5 files changed, 17 insertions(+), 2 deletions(-)
diff --git a/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).png
b/gsoc2022/seagrid-rich-client/Images/Modified_SeaGrid_Overview (2).png
similarity index 100%
rename from gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).png
rename to gsoc2022/seagrid-rich-client/Images/Modified_SeaGrid_Overview (2).png
diff --git a/gsoc2022/seagrid-rich-client/Images/Mol3dEditor.png
b/gsoc2022/seagrid-rich-client/Images/Mol3dEditor.png
new file mode 100644
index ..753a4060
Binary files /dev/null and
b/gsoc2022/seagrid-rich-client/Images/Mol3dEditor.png differ
diff --git a/gsoc2022/seagrid-rich-client/Images/jsme.png
b/gsoc2022/seagrid-rich-client/Images/jsme.png
new file mode 100644
index ..41c14892
Binary files /dev/null and b/gsoc2022/seagrid-rich-client/Images/jsme.png differ
diff --git a/gsoc2022/seagrid-rich-client/Images/nglviewer.png
b/gsoc2022/seagrid-rich-client/Images/nglviewer.png
new file mode 100644
index ..e142a5fe
Binary files /dev/null and b/gsoc2022/seagrid-rich-client/Images/nglviewer.png
differ
diff --git a/gsoc2022/seagrid-rich-client/README.md
b/gsoc2022/seagrid-rich-client/README.md
index 73754958..8f3373a8 100644
--- a/gsoc2022/seagrid-rich-client/README.md
+++ b/gsoc2022/seagrid-rich-client/README.md
@@ -4,7 +4,7 @@
## Architecture of system
-.png)
+.png)
## Steps to Run the Application
### Installation Steps:
@@ -21,7 +21,7 @@
Now to install electronJS run below command.
- - npm install --save-dev electron
+ - npm install electron --save-dev
Run Application
1. Clone the repository.
@@ -31,3 +31,18 @@
3. This will launch the application
4. You can login with your credentials and try to submit the experiment. Also
you can view molecule structures using molecule viewer.
+### Features of Application
+1. Molecule Viewer
+
+
+2. Molecule Editors
+
+ 1. JSME Editor
+
+
+
+ 2. Mol3dEditor
+
+
+
+
[airavata-sandbox] 12/13: external applications added
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 57765045263d1074b6a8b69f034cb4c214f1927a
Author: BECOB257_Aishwarya Sinhasane
AuthorDate: Sun Sep 11 19:45:23 2022 -0400
external applications added
---
gsoc2022/seagrid-rich-client/main.js | 68 ++--
1 file changed, 34 insertions(+), 34 deletions(-)
diff --git a/gsoc2022/seagrid-rich-client/main.js
b/gsoc2022/seagrid-rich-client/main.js
index e2436460..e3d4359c 100644
--- a/gsoc2022/seagrid-rich-client/main.js
+++ b/gsoc2022/seagrid-rich-client/main.js
@@ -10,7 +10,8 @@ const {app, BrowserWindow, MenuItem} = require('electron')
const path = require('path')
const { Menu, dialog, shell } = require('electron')
const defaultMenu = require('electron-default-menu')
-var {spawn} = require('child_process')
+var os = require('os');
+const { win32 } = require('path')
var child = require('child_process').execFile;
function createWindow () {
// Create the browser window.
@@ -37,23 +38,8 @@ function createMolWindow () {
}
})
- // and load the login page for app
- //editorWindow.load("nanocad.html")
editorWindow.loadURL("http://nglviewer.org/ngl/?script=showcase/ferredoxin;)
}
-function createJSMolWindow () {
- // Create the browser window.
- const JSMolWindow = new BrowserWindow({
-width: 800,
-height: 600,
-webPreferences: {
- preload: path.join(__dirname, 'preload.js')
-}
- })
-
- // and load the login page for app
-
JSMolWindow.loadFile("C:\\Users\\aishw\\gsoc\\seagrid-client\\airavata-sandbox\\gsoc2022\\seagrid-rich-client\\ui\\samplemol.html")
-}
function createJSMEWindow(){
const JSMEWindow = new BrowserWindow({
width: 800,
@@ -63,8 +49,10 @@ function createJSMEWindow(){
}
})
- // and load the login page for app
-
JSMEWindow.loadFile("C:\\Users\\aishw\\gsoc\\seagrid-client-electron\\airavata-sandbox\\gsoc2022\\seagrid-rich-client\\JSME\\dist\\index.html")
+ if(process.platform == win32)
+JSMEWindow.loadFile(".\\JSME\\dist\\index.html")
+ else
+JSMEWindow.loadFile("./JSME/dist/index.html")
}
function createMol3DWindow(){
const Mol3DWindow = new BrowserWindow({
@@ -74,19 +62,32 @@ function createMol3DWindow(){
preload: path.join(__dirname, 'preload.js')
}
})
-
- // and load the login page for app
Mol3DWindow.loadURL("https://molview.org/;)
}
function createAvogadro(){
-var executablePath = 'C:\\Program
Files\\Avogadro2\\bin\\avogadro2.exe';
-var parameters = ['Hai', 'Test', 'Dat'];
-child(executablePath, function (err, data) {
+var homedir = process.env.HOME;
+if(os.platform == 'win32')
+ var executablePath = 'C:\\Program Files\\Avogadro2\\bin\\avogadro2.exe';
+else
+ var executablePath = homedir + '/Applications/avogadro2';
+child(executablePath, function (err, data) {
console.log(err)
console.log(data.toString());
-});
+});
+}
+function createVMD(){
+
+ var homedir = process.env.HOME;
+ if(os.platform == 'win32')
+var executablePath = 'C:\\Program Files\\VMD\\vmd.exe';
+ else
+var executablePath = homedir + '/Applications/vmd';
+ child(executablePath, function (err, data) {
+ console.log(err)
+ console.log(data.toString());
+ });
}
// This method will be called when Electron has finished
@@ -100,9 +101,8 @@ app.whenReady().then(() => {
// dock icon is clicked and there are no other windows open.
if (BrowserWindow.getAllWindows().length === 0) createWindow()
})
- const menu = defaultMenu(app, shell);
+ const menu = defaultMenu(app, shell);
-
// Add custom menu
menu.splice(1,0,{
label: 'Molecule Viewer',
@@ -112,12 +112,6 @@ app.whenReady().then(() => {
click: (item, focusedWindow) => {
createMolWindow()
}
- },
- {
-label: 'JSMol Viewer',
-click: (item, focusedWindow) => {
- createJSMolWindow()
-}
}
]
});
@@ -138,14 +132,20 @@ app.whenReady().then(() => {
}
]
});
- menu.splice(2,0,{
-label: 'Avogadro Application',
+ menu.splice(3,0,{
+label: 'External Applications',
submenu: [
{
label: 'Avogadro Editor',
click: (item, focusedWindow) => {
createAvogadro()
}
+ },
+ {
+label: 'VMD',
+click: (item, focusedWindow) => {
+ createVMD()
+}
}
]
});
[airavata-sandbox] 03/13: Delete Modified_SeaGrid_Overview (2).jpg
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 214fbb1fc136264cac5dd1ae3f8f3db8c8591fb3 Author: Aishwarya Vijay Sinhasane <48974593+aishwaryasinhas...@users.noreply.github.com> AuthorDate: Wed Jul 20 16:52:25 2022 -0400 Delete Modified_SeaGrid_Overview (2).jpg --- .../Modified_SeaGrid_Overview (2).jpg | Bin 102337 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).jpg b/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).jpg deleted file mode 100644 index e555b5f5.. Binary files a/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).jpg and /dev/null differ
[airavata-sandbox] 07/13: Update README.md
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 cb7f652f0b5a7e30d91677c66224e0f4b165c12c Author: Aishwarya Vijay Sinhasane <48974593+aishwaryasinhas...@users.noreply.github.com> AuthorDate: Thu Jul 21 03:12:04 2022 -0400 Update README.md --- gsoc2022/seagrid-rich-client/README.md | 7 +-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gsoc2022/seagrid-rich-client/README.md b/gsoc2022/seagrid-rich-client/README.md index 4cd99781..73754958 100644 --- a/gsoc2022/seagrid-rich-client/README.md +++ b/gsoc2022/seagrid-rich-client/README.md @@ -15,15 +15,18 @@ - https://nodejs.org/en/download/ Check node.js installed - - npm -v + + - npm -v - node -v Now to install electronJS run below command. -- npm install --save-dev electron + + - npm install --save-dev electron Run Application 1. Clone the repository. 2. Run below command + - npm start 3. This will launch the application 4. You can login with your credentials and try to submit the experiment. Also you can view molecule structures using molecule viewer.
[airavata-sandbox] 05/13: Create README.md
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 f235532d4ae75e120616fa7cd440db30301bfba1 Author: Aishwarya Vijay Sinhasane <48974593+aishwaryasinhas...@users.noreply.github.com> AuthorDate: Wed Jul 20 16:57:10 2022 -0400 Create README.md --- gsoc2022/seagrid-rich-client/README.md | 15 +++ 1 file changed, 15 insertions(+) diff --git a/gsoc2022/seagrid-rich-client/README.md b/gsoc2022/seagrid-rich-client/README.md new file mode 100644 index ..72b651da --- /dev/null +++ b/gsoc2022/seagrid-rich-client/README.md @@ -0,0 +1,15 @@ +## GSOC 2022 Project + +- **Aishwarya Sinhasane** + +## Architecture of system + +.png) + +## Steps to Run the Application +1. Clone the repository. +2. Run below command + - npm start +3. This will launch the application +4. You can login with your credentials and try to submit the experiment. Also you can view molecule structures using molecule viewer. +
[airavata-sandbox] 02/13: Add files via upload
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 efe17ebb854d1d9e8835d467858573fd2b3d7ecc Author: Aishwarya Vijay Sinhasane <48974593+aishwaryasinhas...@users.noreply.github.com> AuthorDate: Wed Jul 20 16:46:09 2022 -0400 Add files via upload --- .../Modified_SeaGrid_Overview (2).jpg | Bin 0 -> 102337 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).jpg b/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).jpg new file mode 100644 index ..e555b5f5 Binary files /dev/null and b/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).jpg differ
[airavata-sandbox] 08/13: refactored code
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 1dbb954fbaf065ee86ceab4b0624e8bef18b0da3
Author: BECOB257_Aishwarya Sinhasane
AuthorDate: Thu Jul 21 03:43:57 2022 -0400
refactored code
---
gsoc2022/seagrid-rich-client/main.js | 8
gsoc2022/seagrid-rich-client/{ => ui}/1aho.pdb | 0
gsoc2022/seagrid-rich-client/{ => ui/css}/styles.css | 0
gsoc2022/seagrid-rich-client/{ => ui}/nanocad.html | 0
gsoc2022/seagrid-rich-client/{ => ui}/ngl.js | 0
gsoc2022/seagrid-rich-client/{ => ui}/samplemol.html | 1 -
gsoc2022/seagrid-rich-client/{ => ui}/samplengl.html | 0
gsoc2022/seagrid-rich-client/{ => ui}/summary.html | 0
8 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/gsoc2022/seagrid-rich-client/main.js
b/gsoc2022/seagrid-rich-client/main.js
index ab5a06af..b9f64f71 100644
--- a/gsoc2022/seagrid-rich-client/main.js
+++ b/gsoc2022/seagrid-rich-client/main.js
@@ -51,7 +51,7 @@ function createJSMolWindow () {
})
// and load the login page for app
- JSMolWindow.loadFile("samplengl.html")
+
JSMolWindow.loadFile("C:\\Users\\aishw\\gsoc\\airavata-gsoc2022\\airavata-sandbox\\gsoc2022\\seagrid-rich-client\\ui\\samplemol.html")
//editorWindow.loadURL("http://nglviewer.org/ngl/?script=showcase/ferredoxin;)
}
// This method will be called when Electron has finished
@@ -70,16 +70,16 @@ app.whenReady().then(() => {
// Add custom menu
menu.splice(1,0,{
-label: 'Molecule Editor',
+label: 'Molecule Viewer',
submenu: [
{
-label: 'nanocad',
+label: 'NGLViewer',
click: (item, focusedWindow) => {
createMolWindow()
}
},
{
-label: 'JSMol Editor',
+label: 'JSMol Viewer',
click: (item, focusedWindow) => {
createJSMolWindow()
}
diff --git a/gsoc2022/seagrid-rich-client/1aho.pdb
b/gsoc2022/seagrid-rich-client/ui/1aho.pdb
similarity index 100%
rename from gsoc2022/seagrid-rich-client/1aho.pdb
rename to gsoc2022/seagrid-rich-client/ui/1aho.pdb
diff --git a/gsoc2022/seagrid-rich-client/styles.css
b/gsoc2022/seagrid-rich-client/ui/css/styles.css
similarity index 100%
rename from gsoc2022/seagrid-rich-client/styles.css
rename to gsoc2022/seagrid-rich-client/ui/css/styles.css
diff --git a/gsoc2022/seagrid-rich-client/nanocad.html
b/gsoc2022/seagrid-rich-client/ui/nanocad.html
similarity index 100%
rename from gsoc2022/seagrid-rich-client/nanocad.html
rename to gsoc2022/seagrid-rich-client/ui/nanocad.html
diff --git a/gsoc2022/seagrid-rich-client/ngl.js
b/gsoc2022/seagrid-rich-client/ui/ngl.js
similarity index 100%
rename from gsoc2022/seagrid-rich-client/ngl.js
rename to gsoc2022/seagrid-rich-client/ui/ngl.js
diff --git a/gsoc2022/seagrid-rich-client/samplemol.html
b/gsoc2022/seagrid-rich-client/ui/samplemol.html
similarity index 98%
rename from gsoc2022/seagrid-rich-client/samplemol.html
rename to gsoc2022/seagrid-rich-client/ui/samplemol.html
index 953d585d..215220db 100644
--- a/gsoc2022/seagrid-rich-client/samplemol.html
+++ b/gsoc2022/seagrid-rich-client/ui/samplemol.html
@@ -10,7 +10,6 @@
here is structure
-
jmolApplet(400,"load 1aho.pdb","0");
diff --git a/gsoc2022/seagrid-rich-client/samplengl.html
b/gsoc2022/seagrid-rich-client/ui/samplengl.html
similarity index 100%
rename from gsoc2022/seagrid-rich-client/samplengl.html
rename to gsoc2022/seagrid-rich-client/ui/samplengl.html
diff --git a/gsoc2022/seagrid-rich-client/summary.html
b/gsoc2022/seagrid-rich-client/ui/summary.html
similarity index 100%
rename from gsoc2022/seagrid-rich-client/summary.html
rename to gsoc2022/seagrid-rich-client/ui/summary.html
[airavata-sandbox] 09/13: JSME Editor added
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 74b501053d845a23c8659ff43002aab9c12b03d6
Author: BECOB257_Aishwarya Sinhasane
AuthorDate: Tue Jul 26 14:34:13 2022 -0400
JSME Editor added
---
gsoc2022/seagrid-rich-client/JSME-webpack-example | 1 +
gsoc2022/seagrid-rich-client/main.js | 18 +++---
gsoc2022/seagrid-rich-client/ngl | 1 -
gsoc2022/seagrid-rich-client/package-lock.json| 14 +++---
gsoc2022/seagrid-rich-client/package.json | 2 +-
5 files changed, 24 insertions(+), 12 deletions(-)
diff --git a/gsoc2022/seagrid-rich-client/JSME-webpack-example
b/gsoc2022/seagrid-rich-client/JSME-webpack-example
new file mode 16
index ..07b3a035
--- /dev/null
+++ b/gsoc2022/seagrid-rich-client/JSME-webpack-example
@@ -0,0 +1 @@
+Subproject commit 07b3a035775fc3f5b6cb7b2dc0288e68d123e1c9
diff --git a/gsoc2022/seagrid-rich-client/main.js
b/gsoc2022/seagrid-rich-client/main.js
index b9f64f71..c0dad527 100644
--- a/gsoc2022/seagrid-rich-client/main.js
+++ b/gsoc2022/seagrid-rich-client/main.js
@@ -54,6 +54,18 @@ function createJSMolWindow () {
JSMolWindow.loadFile("C:\\Users\\aishw\\gsoc\\airavata-gsoc2022\\airavata-sandbox\\gsoc2022\\seagrid-rich-client\\ui\\samplemol.html")
//editorWindow.loadURL("http://nglviewer.org/ngl/?script=showcase/ferredoxin;)
}
+function createJSMEWindow(){
+ const JSMEWindow = new BrowserWindow({
+width: 800,
+height: 600,
+webPreferences: {
+ preload: path.join(__dirname, 'preload.js')
+}
+ })
+
+ // and load the login page for app
+
JSMEWindow.loadFile("C:\\Users\\aishw\\gsoc\\airavata-gsoc2022\\airavata-sandbox\\gsoc2022\\seagrid-rich-client\\JSME-webpack-example\\dist\\index.html")
+}
// This method will be called when Electron has finished
// initialization and is ready to create browser windows.
// Some APIs can only be used after this event occurs.
@@ -87,12 +99,12 @@ app.whenReady().then(() => {
]
});
menu.splice(2,0,{
-label: 'Applicaion Editor',
+label: 'Molecule Editor',
submenu: [
{
-label: 'G09',
+label: 'JSME Editor',
click: (item, focusedWindow) => {
- dialog.showMessageBox({message: 'Do something', buttons: ['OK'] });
+ createJSMEWindow()
}
}
]
diff --git a/gsoc2022/seagrid-rich-client/ngl b/gsoc2022/seagrid-rich-client/ngl
deleted file mode 16
index bd4a31c7..
--- a/gsoc2022/seagrid-rich-client/ngl
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit bd4a31c72e007d170b6bae298a5f7c976070e173
diff --git a/gsoc2022/seagrid-rich-client/package-lock.json
b/gsoc2022/seagrid-rich-client/package-lock.json
index 5c554ad9..23fdf74a 100644
--- a/gsoc2022/seagrid-rich-client/package-lock.json
+++ b/gsoc2022/seagrid-rich-client/package-lock.json
@@ -13,7 +13,7 @@
"ngl": "^0.10.4"
},
"devDependencies": {
-"electron": "^19.0.4"
+"electron": "^19.0.9"
}
},
"node_modules/@electron/get": {
@@ -251,9 +251,9 @@
"dev": true
},
"node_modules/electron": {
- "version": "19.0.4",
- "resolved": "https://registry.npmjs.org/electron/-/electron-19.0.4.tgz;,
- "integrity":
"sha512-roRYr1VNAWIhjD9n8qZdmhROtrzsFpuZEXrjWAw+GqPbZlrUInmvFCviRDC2Lt+VBsTNRpTfPpfzXSlLL4reEw==",
+ "version": "19.0.9",
+ "resolved": "https://registry.npmjs.org/electron/-/electron-19.0.9.tgz;,
+ "integrity":
"sha512-ooEwrv8Y7NSzdhKcl6kPCYecnzcg5nFWuS5ryG+VFH3MMBR8zXh9nW2wLsZrBz6OGUxXrcc5BKBC7dA8C6RhGQ==",
"dev": true,
"hasInstallScript": true,
"dependencies": {
@@ -1184,9 +1184,9 @@
"dev": true
},
"electron": {
- "version": "19.0.4",
- "resolved": "https://registry.npmjs.org/electron/-/electron-19.0.4.tgz;,
- "integrity":
"sha512-roRYr1VNAWIhjD9n8qZdmhROtrzsFpuZEXrjWAw+GqPbZlrUInmvFCviRDC2Lt+VBsTNRpTfPpfzXSlLL4reEw==",
+ "version": "19.0.9",
+ "resolved": "https://registry.npmjs.org/electron/-/electron-19.0.9.tgz;,
+ "integrity":
"sha512-ooEwrv8Y7NSzdhKcl6kPCYecnzcg5nFWuS5ryG+VFH3MMBR8zXh9nW2wLsZrBz6OGUxXrcc5BKBC7dA8C6RhGQ==",
"dev": true,
"requires": {
"@electron/get": "^1.14.1",
diff --git a/gsoc2022/seagrid-rich-client/package.json
b/gsoc2022/seagrid-rich-client/package.json
index 85007893..f8a00601 100644
--- a/gsoc2022/seagrid-rich-client/package.json
+++ b/gsoc2022/seagrid-rich-client/package.json
@@ -16,7 +16,7 @@
"author": "Aishwarya",
"license": "CC0-1.0",
"devDependencies": {
-"electron": "^19.0.4"
+"electron": "^19.0.9"
},
"dependencies": {
"electron-default-menu": "^1.0.2",
[airavata-sandbox] 04/13: Add files via upload
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 6ef0d0706b98240dbbc7766651221c6831316804 Author: Aishwarya Vijay Sinhasane <48974593+aishwaryasinhas...@users.noreply.github.com> AuthorDate: Wed Jul 20 16:52:40 2022 -0400 Add files via upload --- .../Modified_SeaGrid_Overview (2).png | Bin 0 -> 313195 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).png b/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).png new file mode 100644 index ..23503ce4 Binary files /dev/null and b/gsoc2022/seagrid-rich-client/Modified_SeaGrid_Overview (2).png differ
[airavata-data-lake] branch master updated: Fixing shared_by
This is an automated email from the ASF dual-hosted git repository.
isjarana pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata-data-lake.git
The following commit(s) were added to refs/heads/master by this push:
new 47f5248 Fixing shared_by
new 39dfbbd Merge pull request #166 from isururanawaka/mysql_conversion
47f5248 is described below
commit 47f52480672f27598c65f74b8de527836af469dc
Author: Isuru Ranawaka
AuthorDate: Mon Sep 12 10:37:35 2022 -0400
Fixing shared_by
---
.../drms/api/handlers/ResourceServiceHandler.java| 16 +---
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git
a/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
b/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
index d9be5bc..ef3b1e4 100644
---
a/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
+++
b/data-resource-management-service/drms-rdbms-impl/drms-server/src/main/java/org/apache/airavata/drms/api/handlers/ResourceServiceHandler.java
@@ -284,16 +284,18 @@ public class ResourceServiceHandler extends
ResourceServiceGrpc.ResourceServiceI
for (ResourceSearchQuery searchQuery : resourceSearchQueries) {
-SearchCriteria searchCriteria = SearchCriteria.newBuilder()
-
.setSearchField(EntitySearchField.valueOf(searchQuery.getField()))
-
.setCondition(SearchCondition.valueOf(searchQuery.getOptions()))
-.setValue(searchQuery.getValue()).build();
+if(!searchQuery.getField().equals("shared_with")) {
+SearchCriteria searchCriteria = SearchCriteria.newBuilder()
+
.setSearchField(EntitySearchField.valueOf(searchQuery.getField()))
+
.setCondition(SearchCondition.valueOf(searchQuery.getOptions()))
+.setValue(searchQuery.getValue()).build();
-searchRequestBuilder =
searchRequestBuilder.addSearchCriteria(searchCriteria);
+searchRequestBuilder =
searchRequestBuilder.addSearchCriteria(searchCriteria);
+}
}
-if (resourceSearchQueries.isEmpty()) {
+//if (resourceSearchQueries.isEmpty()) {
String type = request.getType();
@@ -314,7 +316,7 @@ public class ResourceServiceHandler extends
ResourceServiceGrpc.ResourceServiceI
.setCondition(SearchCondition.EQUAL)
.setValue(type).build());
}
-}
+//}
SearchRequest searchRequest = searchRequestBuilder.setOwnerId(callUser
.getUsername())
[airavata-custos] branch baremetal updated: Add shared_by attribute to sharing core service
This is an automated email from the ASF dual-hosted git repository.
isjarana pushed a commit to branch baremetal
in repository https://gitbox.apache.org/repos/asf/airavata-custos.git
The following commit(s) were added to refs/heads/baremetal by this push:
new 90ae296d Add shared_by attribute to sharing core service
new 79ce2272 Merge pull request #306 from isururanawaka/baremetal
90ae296d is described below
commit 90ae296db1f5252a22f12068b7ac29e9af7930bc
Author: Isuru Ranawaka
AuthorDate: Mon Sep 12 10:29:47 2022 -0400
Add shared_by attribute to sharing core service
---
.../sharing-core-service/src/main/proto/SharingService.proto | 1 +
1 file changed, 1 insertion(+)
diff --git
a/custos-core-services/sharing-core-service/src/main/proto/SharingService.proto
b/custos-core-services/sharing-core-service/src/main/proto/SharingService.proto
index c11f6ac5..b72bbc99 100644
---
a/custos-core-services/sharing-core-service/src/main/proto/SharingService.proto
+++
b/custos-core-services/sharing-core-service/src/main/proto/SharingService.proto
@@ -44,6 +44,7 @@ enum EntitySearchField {
PARENT_ID = 8;
SHARED_COUNT = 9;
PERMISSION_TYPE_ID = 10;
+SHARED_BY=11;
}
