Doc Issues 8

client/test/README.md

@@ -114,7 +114,7 @@ window.env = {
 };
 ```
 
-## test/.env
+## test/.env - localhost
 
 ```ini
 REACT_APP_TEST_USERNAME=TestUsername
@@ -156,7 +156,7 @@ window.env = {
 };
 ```
 
-## test/.env
+## test/.env - Integration server
 
 ```ini
 REACT_APP_TEST_USERNAME=TestUsername

docs/LICENSE.md

@@ -1,33 +1,35 @@
+# License
+
 --- Start of Definition of INTO-CPS Association Public License ---
 
 /*
 
 * This file is part of the INTO-CPS Association.
- 
+
 * Copyright (c) 2017-CurrentYear, INTO-CPS Association (ICA),
 * c/o Peter Gorm Larsen, Aarhus University, Department of Engineering,
 * Finlandsgade 22, 8200 Aarhus N, Denmark.
- 
+
 * All rights reserved.
- 
+
 * THIS PROGRAM IS PROVIDED UNDER THE TERMS OF GPL VERSION 3 LICENSE OR
 * THIS INTO-CPS ASSOCIATION PUBLIC LICENSE (ICAPL) VERSION 1.0.
 * ANY USE, REPRODUCTION OR DISTRIBUTION OF THIS PROGRAM CONSTITUTES
 * RECIPIENT'S ACCEPTANCE OF THE INTO-CPS ASSOCIATION PUBLIC LICENSE OR
 * THE GPL VERSION 3, ACCORDING TO RECIPIENTS CHOICE.
- 
+
 * The INTO-CPS tool suite software and the INTO-CPS Association
 * Public License (ICAPL) are obtained from the INTO-CPS Association, either
 * from the above address, from the URLs: <http:>http://www.into-cps.org</http:> or
 * in the INTO-CPS tool suite distribution.
 * GNU version 3 is obtained from: <http:>http://www.gnu.org/copyleft/gpl.html</http:>.
- 
+
 * This program is distributed WITHOUT ANY WARRANTY; without
 * even the implied warranty of  MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE, EXCEPT AS EXPRESSLY SET FORTH
 * IN THE BY RECIPIENT SELECTED SUBSIDIARY LICENSE CONDITIONS OF
 * THE INTO-CPS ASSOCIATION PUBLIC LICENSE.
- 
+
 * See the full ICAPL conditions for more details.
 
  */

docs/admin/client/CLIENT.md

@@ -29,7 +29,6 @@ To host DTaaS client website on your server, follow these steps:
     REACT_APP_WORKBENCHLINK_JUPYTERLAB: "Endpoint for the Jupyter Lab link",
     REACT_APP_WORKBENCHLINK_JUPYTERNOTEBOOK:
       "Endpoint for the Jupyter Notebook link",
-
     REACT_APP_CLIENT_ID: 'AppID genereated by the gitlab OAuth provider',
     REACT_APP_AUTH_AUTHORITY: 'URL of the private gitlab instance',
     REACT_APP_REDIRECT_URI: 'URL of the homepage for the logged in users of the website',
@@ -49,7 +48,6 @@ To host DTaaS client website on your server, follow these steps:
     REACT_APP_WORKBENCHLINK_VSCODE: '/tools/vscode/',
     REACT_APP_WORKBENCHLINK_JUPYTERLAB: '/lab',
     REACT_APP_WORKBENCHLINK_JUPYTERNOTEBOOK: '',
-
     REACT_APP_CLIENT_ID: '934b98f03f1b6f743832b2840bf7cccaed93c3bfe579093dd0942a433691ccc0',
     REACT_APP_AUTH_AUTHORITY: 'https://gitlab.foo.com/',
     REACT_APP_REDIRECT_URI: 'https://foo.com/Library',
@@ -70,7 +68,6 @@ To host DTaaS client website on your server, follow these steps:
     REACT_APP_WORKBENCHLINK_VSCODE: '/tools/vscode/',
     REACT_APP_WORKBENCHLINK_JUPYTERLAB: '/lab',
     REACT_APP_WORKBENCHLINK_JUPYTERNOTEBOOK: '',
-
     REACT_APP_CLIENT_ID: '934b98f03f1b6f743832b2840bf7cccaed93c3bfe579093dd0942a433691ccc0',
     REACT_APP_AUTH_AUTHORITY: 'https://gitlab.foo.com/',
     REACT_APP_REDIRECT_URI: 'https://foo.com/bar/Library',

docs/admin/servers/lib/LIB-MS.md

@@ -288,9 +288,7 @@ POST /lib HTTP/1.1
 Host: localhost:4001
 Content-Type: application/json
 Content-Length: 388
-{
-   "query":"query {\n  listDirectory(path: \"user1\") {\n    repository {\n      tree {\n        blobs {\n          edges {\n            node {\n              name\n              type\n            }\n          }\n        }\n        trees {\n          edges {\n            node {\n              name\n              type\n            }\n          }\n        }\n      }\n    }\n  }\n}"
-}
+{"query":"query {\n  listDirectory(path: \"user1\") {\n    repository {\n      tree {\n        blobs {\n          edges {\n            node {\n              name\n              type\n            }\n          }\n        }\n        trees {\n          edges {\n            node {\n              name\n              type\n            }\n          }\n        }\n      }\n    }\n  }\n}"}
 ```
 
 This HTTP POST request will generate the following HTTP response message.
@@ -318,9 +316,7 @@ POST /lib HTTP/1.1
 Host: localhost:4001
 Content-Type: application/json
 Content-Length: 217
-{
-   "query":"query {\n  readFile(path: \"user2/data/welcome.txt\") {\n    repository {\n      blobs {\n        nodes {\n          name\n          rawBlob\n          rawTextBlob\n        }\n      }\n    }\n  }\n}"
-}
+{"query":"query {\n  readFile(path: \"user2/data/welcome.txt\") {\n    repository {\n      blobs {\n        nodes {\n          name\n          rawBlob\n          rawTextBlob\n        }\n      }\n    }\n  }\n}"}
 ```
 
 ```http

docs/admin/services.md

@@ -51,7 +51,8 @@ docker exec rabbitmq-server rabbitmqctl set_permissions -p "/<vhost>" <username>
 ```
 
 The RabbitMQ service requires raw TCP/UDP protocol access to network.
-The default Traefik configuration of DTaaS does not permit TCP/UDP traffic. There are two possible choices here:
+The default Traefik configuration of DTaaS does not permit
+TCP/UDP traffic. There are two possible choices here:
 
 * Configure Traefik gateway to permit TCP/UDP traffic
 * Bypass Traefik altogether for RabbitMQ service
@@ -94,7 +95,7 @@ printf "Complete the setup from GUI"
 
 The user credentials have also been set in the command as:
 
-**username**: admin  
+**username**: admin
 **password**: DTaaSGrafana
 
 Remember to change these credentials before starting the docker container.
@@ -122,7 +123,7 @@ docker run -d -p 80:8086 \
 
 The user credentials have also been set in the command as:
 
-**username**: dtaas  
+**username**: dtaas
 **password**: dtaas1357
 
 Remember to change these credentials before starting the docker container.

docs/developer/index.md

@@ -46,51 +46,61 @@ a development workflow is in place. Each developer should follow these steps:
 
 1. Fork of the main repository into your github account.
 1. Setup
-[Code Climate](https://docs.codeclimate.com/docs/getting-started-with-code-climate)
-and
-[Codecov](https://docs.codecov.com/docs/quick-start)
-for your fork. The codecov does not require secret token
-for public repositories.
+   [Code Climate](https://docs.codeclimate.com/docs/getting-started-with-code-climate)
+   and
+   [Codecov](https://docs.codecov.com/docs/quick-start)
+   for your fork. The codecov does not require secret token
+   for public repositories.
 1. Install git-hooks for the project.
 1. Use
-[Fork, Branch, PR](https://gun.io/news/2017/01/how-to-github-fork-branch-and-pull-request/)
-workflow.
+   [Fork, Branch, PR](https://gun.io/news/2017/01/how-to-github-fork-branch-and-pull-request/)
+   workflow.
 1. Work in your fork and open a PR from your working branch to your `feature/distributed-demo` branch.
-The PR will run all the github actions, code climate and codecov checks.
+   The PR will run all the github actions, code climate and codecov checks.
 1. Resolve all the issues identified in the previous step.
 1. If you have access to the
-[integration server](https://github.com/INTO-CPS-Association/DTaaS/wiki/DTaaS-Integration-Server),
-try your working branch on the integration server.
+   [integration server](https://github.com/INTO-CPS-Association/DTaaS/wiki/DTaaS-Integration-Server),
+   try your working branch on the integration server.
 1. Once changes are verified, a PR should be made to the `feature/distributed-demo` branch of
-the upstream
-[DTaaS repository](https://github.com/into-cps-association/DTaaS).
+   the upstream
+   [DTaaS repository](https://github.com/into-cps-association/DTaaS).
 1. The PR will be merged after checks by either the project administrators or the maintainers.
 
-Remember that every PR should be meaningful and satisfies a well-defined user story or improve
+Remember that every PR should be meaningful and satisfies
+a well-defined user story or improve
 the code quality.
 
 ## :eye: Code Quality
 
 The project code qualities are measured based on:
 
 * Linting issues identified by
-[Code Climate](https://codeclimate.com/github/INTO-CPS-Association/DTaaS)
+  [Code Climate](https://codeclimate.com/github/INTO-CPS-Association/DTaaS)
 * Test coverage report collected by
-[Codecov](https://codecov.io/gh/INTO-CPS-Association/DTaaS)
+  [Codecov](https://codecov.io/gh/INTO-CPS-Association/DTaaS)
 * Successful [github actions](https://github.com/INTO-CPS-Association/DTaaS/actions)
 
 ### Code Climate
 
-Code Climate performs static analysis, linting and style checks. Quality checks are performed by codeclimate are to ensure the best possible quality of code to add to our project.
+Code Climate performs static analysis, linting and style checks.
+Quality checks are performed by codeclimate are to ensure the best
+possible quality of code to add to our project.
 
-While any new issues introduced in your code would be shown in the PR page itself, to address any specific issue, you can visit the issues or code section of the codeclimate page.
+While any new issues introduced in your code would be
+shown in the PR page itself, to address any specific issue,
+you can visit the issues or code section of the codeclimate page.
 
-It is highly recommended that any code you add does not introduce new quality issues. If they are introduced, they should be fixed immediately using the appropriate suggestions from Code Climate, or in worst case, adding a ignore flag (To be used with caution).
+It is highly recommended that any code you add does
+not introduce new quality issues. If they are introduced,
+they should be fixed immediately using the appropriate suggestions
+from Code Climate, or in worst case, adding a ignore flag
+(To be used with caution).
 
 ### Codecov
 
 Codecov keeps track of the test coverage for the entire project.
-For information about testing and workflow related to that, please see the [testing page](testing/intro.md).
+For information about testing and workflow related to that,
+please see the [testing page](testing/intro.md).
 
 ### Github Actions
 

docs/developer/servers/lib/lib-ms.md

@@ -77,11 +77,11 @@ classDiagram
 sequenceDiagram
     actor Client
     actor Traefik
-    
+
     box LightGreen Library Microservice
     participant FR as FilesResolver
     participant FSF as FilesServiceFactory
-    participant CS as ConfigService 
+    participant CS as ConfigService
     participant IFS as IFilesService
     participant LFS as LocalFilesService
     participant GFS as GitlabFilesService

docs/developer/system/architecture.md

@@ -3,29 +3,33 @@
 ## User Requirements
 
 The DTaaS software platform users expect a single platform
-to support the complete DT lifecycle. To be more precise, the platform users expect the following features:
+to support the complete DT lifecycle. To be more precise,
+the platform users expect the following features:
 
 1. **Author** – create different assets of the DT on the
-platform itself. This step requires use of some software
-frameworks and tools whose sole purpose is to author
-DT assets.
+   platform itself. This step requires use of some software
+   frameworks and tools whose sole purpose is to author
+   DT assets.
 1. **Consolidate** – consolidate the list of available DT assets
-and authoring tools so that user can navigate the library
-of reusable assets. This functionality requires support
-for discovery of available assets.
+   and authoring tools so that user can navigate the library
+   of reusable assets. This functionality requires support
+   for discovery of available assets.
 1. **Configure** – support selection and configuration of
-DTs. This functionality also requires support for validation of a given configuration.
-1. **Execute** – provision computing infrastructure on demand to support execution of a DT.
+   DTs. This functionality also requires support for validation
+   of a given configuration.
+1. **Execute** – provision computing infrastructure on demand to
+   support execution of a DT.
 1. **Explore** – interact with a DT and explore the results
-stored both inside and outside the platform. Exploration
-may lead to analytical insights.
+   stored both inside and outside the platform. Exploration
+   may lead to analytical insights.
 1. **Save** – save the state of a DT that’s already in the
-execution phase. This functionality is required for ondemand saving and re-spawning of DTs.
+   execution phase. This functionality is required for on
+   demand saving and re-spawning of DTs.
 1. **What-if analysis** – explore alternative scenarios to (i)
-plan for an optimal next step, (ii) recalibrate new DT
-assets, (iii) automated creation of new DTs or their
-assets; these newly created DT assets may be used to
-perform scientifically valid experiments.
+   plan for an optimal next step, (ii) recalibrate new DT
+   assets, (iii) automated creation of new DTs or their
+   assets; these newly created DT assets may be used to
+   perform scientifically valid experiments.
 1. **Share** – share a DT with other users of their organisation.
 
 ## System Architecture
@@ -41,7 +45,7 @@ The gateway is a single point of entry for direct access to the platform
 services. The gateway is responsible for controlling user access to
 the microservice components. The service mesh
 enables discovery of microservices, load balancing and authentication
-functionalities.  
+functionalities.
 
 In addition, there are microservices for catering to author, store,
 explore, configure, execute and scenario analysis requirements.
@@ -51,30 +55,29 @@ core requirements of the system.
 The microservices responsible for satisfying the user requirements are:
 
 1. **The security microservice** implements
-role-based access control (RBAC) in the platform.
+   role-based access control (RBAC) in the platform.
 1. **The accounting microservice** is responsible for keeping track of the
-platform, DT asset and infrastructure usage. Any licensing,
-usage restrictions need to be enforced by the accounting
-microservice. Accounting is a pre-requisite to commercialisation of
-the platform.
-
-    Due to significant use of external
-infrastructure and resources via the platform, the accounting
-microservice needs to interface with accounting systems of
-the external services.
+   platform, DT asset and infrastructure usage. Any licensing,
+   usage restrictions need to be enforced by the accounting
+   microservice. Accounting is a pre-requisite to commercialisation of
+   the platform.
+   Due to significant use of external
+   infrastructure and resources via the platform, the accounting
+   microservice needs to interface with accounting systems of
+   the external services.
 
 1. **The data microservice** is a frontend to all the databases
-integrated into the platform. A time-series database and a
-graph database are essential. These two databases store timeseries
-data from PT, events on PT/DT, commands sent by
-DT to PT. The PTs uses these databases even when their
-respective DTs are not in the execute phase.
+   integrated into the platform. A time-series database and a
+   graph database are essential. These two databases store timeseries
+   data from PT, events on PT/DT, commands sent by
+   DT to PT. The PTs uses these databases even when their
+   respective DTs are not in the execute phase.
 1. **The visualisation microservice** is again a frontend to
-visualisation software that are natively supported inside the platform.
-Any visualisation software running either on external
-systems or on client browsers do not need to interact with
-this microservice. They can directly use the data provided by
-the data microservice.
+   visualisation software that are natively supported inside the platform.
+   Any visualisation software running either on external
+   systems or on client browsers do not need to interact with
+   this microservice. They can directly use the data provided by
+   the data microservice.
 
 ## C4 Architectural Diagrams
 

docs/developer/system/current-status.md

@@ -81,7 +81,7 @@ based on these services.
 The development priorities for the DTaaS software development team are:
 
 * [DT Runner](https://github.com/INTO-CPS-Association/DTaaS/tree/feature/distributed-demo/servers/execution/runner)
-(API Interface to DT)
+  (API Interface to DT)
 * Multi-user and microservice security
 * Increased automation of installation procedures
 * DT Configuration DSL ín the form of YAML schema