[159111761] Getting Started Docs (#47)

* [159111761] Getting Started Docs

- Add documentation for getting stated with the application 
- Add config.properties template
- Minor fixes to the read me document

BackendWebApp/README.md

@@ -5,7 +5,54 @@ Bio-studies web application provides http services used by submission tool and w
 1. Temporally data storing
 1. Security login and access check
 
-# How to generate artifacts
+## Getting Started
+
+### Dependencies
+In order to build and execute the application in your local environment, it's necessary to have the following
+dependencies installed:
+* Java SDK (version 8 at least)
+* Gradle 4.7
+* Docker 
+
+ >Notes: <br/>
+ Oracle Java should be used instead of openJDK <br/>
+ Docker needs to be configured to be used without super user privileges. Check
+ [here](https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user) for more info.
+ 
+ ### Application Setup
+ Once the dependencies mentioned above are up and running, please follow these steps to configure the application:
+ 1. Clone the repository
+ 2. Go to the app directory
+ 3. Execute `gradle build`
+ 4. Move to `BackendWebApp` folder
+ 5. Execute `gradle setUpDatabase`
+ 6. In a different location from the repository, create a folder which will be used as the **nfs** folder
+ 7. Go to `BackendWebApp/src/test/resources/nfs/templates` directory
+ 8. Copy the `config.properties` file into the **nfs** folder, created in step 6
+ 9. Replace `${BASE_PATH}` with the actual path for the **nfs** folder
+ 10. Open `BackendWebApp/src/main/resources/application.yml` file
+ 11. Set the `baseDir` property to the path for the **nfs** folder
+ 12. Go back to root directory
+ 13. Execute `gradle bootRun`
+ 14. The application should now be up and running at
+ [http://localhost:8586/biostd/test/testLogin.html](http://localhost:8586/biostd/test/testLogin.html)
+
+### Session Key
+There are two mechanisms to get a session key to be used for the requests to the backend:
+
+* **Command Line:**
+  1. Inside `BackendWebApp` folder execute `gradle getAuthToken`
+  2. Copy the value after **Session Key:**
+  
+* **UI:**
+  1. Go to [http://localhost:8586/biostd/test/testLogin.html](http://localhost:8586/biostd/test/testLogin.html)
+  2. Type the username `admin_user@ebi.ac.uk`
+  3. Type the password `123456` (yes, we know, remember this is a local instance :grimacing:)
+  4. Leave the PassHash field empty
+  5. Click `Login`
+  6. Copy the value after **Session Key:**
+
+## How to generate artifacts
 Both war and jar deployment type is supported only execute build command
 
     gradle bootJar

BackendWebApp/src/test/resources/nfs/templates/config.properties

+db.hibernate.cache.use_query_cache=false
+db.hibernate.cache.use_second_level_cache=false
+db.hibernate.ejb.discard_pc_on_close=true
+db.hibernate.connection.url=jdbc:mysql://localhost:3306/BioStudiesDev?useSSL=false
+db.hibernate.dialect=org.hibernate.dialect.MySQLDialect
+db.hibernate.connection.username=root
+db.hibernate.connection.password=admin
+db.hibernate.connection.driver_class=com.mysql.jdbc.Driver
+db.hibernate.hbm2ddl.auto=none
+db.hibernate.c3p0.max_size=20
+db.hibernate.c3p0.min_size=0
+db.hibernate.c3p0.timeout=5000
+db.hibernate.c3p0.max_statements=50
+db.hibernate.c3p0.idle_test_period=300
+db.hibernate.c3p0.acquire_increment=2
+db.hibernate.show_sql=true
+db.hibernate.search.default.indexBase=index
+db.hibernate.search.default.directory_provider=filesystem
+db.hibernate.search.lucene_version=LUCENE_54
+biostd.createFileStructure=true
+biostd.enableUnsafeRequests=true
+biostd.workDir=temp
+biostd.userGroupDir=dropbox
+biostd.userGroupIndexDir=ugindex
+biostd.submissionDir=submission
+biostd.submissionHistoryDir=history
+biostd.submissionTransactionDir=transaction
+biostd.publicFTPDir=${BASE_PATH}/FTP
+biostd.updateDir=updates
+biostd.updateWaitPeriod=30
+biostd.defaultSubmissionAccNoPrefix=SBMd-
+biostd.defaultSubmissionAccNoSuffix=-def
+biostd.mandatoryAccountActivation=false
+biostd.dataMountPath=/data
+biostd.recapcha_private_key=6Lcmlv0SAAAAANysy6M8YdozfJnOQxc2JB9WaOS1
+

BackendWebApp/src/test/resources/scripts/getAuthToken.sh

@@ -7,4 +7,4 @@ RESPONSE=$(curl -s \
 
 TOKEN=$(echo $RESPONSE | python -c 'import sys, json; print json.load(sys.stdin)["sessid"]');
 
-echo "Auth Token: $TOKEN";
+echo "Session Key: $TOKEN";

README.md

@@ -2,7 +2,7 @@
 
 ## Modules
 ### Backend Web App
-Java application that support bio studies data submission thought http web services.
+Java application that supports the bio studies data submission thought http web services.
 
 ### Core Model
 Contains model/database representation classes of Bio-Studies backend application.
@@ -14,13 +14,13 @@ Contains utility methods and classes.
 Contains utility methods and classes used to read submissions input files.
 
 ### Submit Tools
-Help perform submissions thought terminal
+Helps to perform submissions through terminal
 
 ### Convert tool
-Helps to converts between different submissions formats
+Helps to convert between different submissions formats
 
 ## Coding standards
-Project follow google [java coding standards](https://google.github.io/styleguide/javaguide.html)
+The project follows the google [java coding standards](https://google.github.io/styleguide/javaguide.html)
 
 - [Eclipse formatter](https://github.com/google/styleguide/blob/gh-pages/eclipse-java-google-style.xml)
 - [Idea formatter](https://github.com/google/styleguide/blob/gh-pages/intellij-java-google-style.xml)
@@ -30,7 +30,7 @@ Project follow google [java coding standards](https://google.github.io/styleguid
 
 ### Importing project
 
-import as gradle project in your favorite IDE
+Import as gradle project in your favorite IDE
 
 
 ### Generating artifact
@@ -43,4 +43,3 @@ Run gradle build command either using local distribution or wrapper
  ```
 
 Generated war will be available under `BackendWebApp/builds/libs` folder. 
-