Merge pull request #742 from molgenis/docs/english

docs: reviewed and corrected/improved English

CONTRIBUTING.md

@@ -21,7 +21,7 @@ We use gradle to build:
 ./gradlew run
 ```
 
-As we now have the option to download the logfile from the application we need to have one to begin with!
+As we now have the option to download the logfile from the application we need to have one to begin with:
 
 ```bash
 # Leave out the -a to overwrite instead of append
@@ -90,7 +90,7 @@ We have several components
 
 ## Releasing
 
-Releases are done whenever the versionnumber gets bumped. For more information see the `Commit messages and versioning (Major, Minor, Patch updates)` section below.
+Releases are done whenever the version number gets bumped. For more information see the `Commit messages and versioning (Major, Minor, Patch updates)` section below.
 
 We use mooltiverse [Nyx](https://mooltiverse.github.io/nyx/guide/user/introduction/how-nyx-works/) for changelog and publishing to github.
 
@@ -102,7 +102,7 @@ Use `./gradlew nyxMake` to see what is build in [build/distributions](./build/di
 
 Versionnumbers are updated according to [Semantic versioning](https://semver.org/), using [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/). 
 
-Please be aware that only new releases will be done when one of the above prefixes is used. 
+Please be aware that new releases will only be done when one of the above prefixes is used. 
 
 Other prefixes do not indicate user-facing changes and will therefore not result in a version bump, consequently not resulting in a new (pre) release. 
 
@@ -131,8 +131,8 @@ git log --pretty=format:"%s" | cut -d: -f1 | sort | uniq -c | sort -n
 
 ## Continuous integration
 
-- we test on each PR and merges on master
-- we build docker compose set for CI testing and demo purposes.
+- We test on each PR and merges on master
+- We build docker compose set for CI testing and demo purposes.
   - [CI testing](./docker/ci/README.md)
   - Demo zip file is a delivery you as artifact
   - Master build have a armadillo-compose.zip for download

armadillo/src/main/java/org/molgenis/armadillo/README.md

@@ -20,7 +20,7 @@ This layer is likely responsible for data persistence.
 
 ## security
 
-This layer is likely responsible for authentication and authorization.
+This layer is likely responsible for authentication and authorisation.
 
 ## exceptions
 

docker/ci/Dockerfile

@@ -11,7 +11,7 @@ RUN install2.r --skipinstalled --repo https://cloud.r-project.org devtools diffo
 
 RUN install2.r --skipinstalled --repo https://cloud.r-project.org arrow future RCurl cli
 
-RUN install2.r --skipinstalled --repo https://cloud.r-project.org DSI resourcer MolgenisArmadillo DSMolgenisArmadillo
+RUN install2.r --repo https://cloud.r-project.org DSI resourcer MolgenisArmadillo DSMolgenisArmadillo
 
 RUN mkdir -p /cicd/armadillo/scripts/release
 

docker/ci/armadillo-compose.md

@@ -2,7 +2,7 @@
 
 To use this zip content you need to
 - have Docker (desktop) installed
-- being able to run `docker compose` from the terminal
+- be able to run `docker compose` from the terminal
 - cd into the `docker-compose` directory
 
 ## Start
@@ -31,7 +31,7 @@ docker compose up
 
 This will show all messages from all running images. To stop you need to use `CTRL-C` or use the stop step below.
 
-If you don't want to see these `docker compose up --detach`
+If you don't want to see these messages `docker compose up --detach`
 
 ## Login
 

docs/README.md

@@ -2,7 +2,7 @@
 
 Use MOLGENIS/Armadillo to make data available for privacy protecting federated analysis using [DataSHIELD](https://datashield.org) protocol. Armadillo
 service provides the following features:
-* **manage data projects**. Projects can either hold tabular data in the efficient 'parquet' format or any other file use DataSHIELD
+* **manage data projects**. Projects can either hold tabular data in the efficient 'parquet' format or any other file using the DataSHIELD
   'resources' framework.
 * **grant users access permission**. We use a central OIDC service like KeyCloak or FusionAuth in combination with a trused identity provider like
   Life Sciences AAI to authenticate users.

docs/faq.md

@@ -8,7 +8,6 @@ Instead of making Armadillo start/stop DataSHIELD profiles you can also use dock
 See commented section in docker-compose.yml file.
 
 ## Can I pass environment or commandline variables instead of application.yml?
-
 Yes, it is standard spring. 
 
 ## Can I run Armadillo with oauth2 config offline?
@@ -17,38 +16,35 @@ Yes, you can run in 'offline' profile
 ./gradlew run -Dspring.profiles.active=offline
 ```
 
-## How to run previous armadillo 2?
+## How to run Armadillo version 2?
 
 For armadillo 2.x you can follow instructions at
 * for testing we use docker compose at https://github.com/molgenis/molgenis-service-armadillo/tree/armadillo-service-2.2.3
 * for production we are using Ansible at https://galaxy.ansible.com/molgenis/armadillo`
 
 ## How to run Armadillo as developer?
-
 We develop Armadillo using IntelliJ.
 
 ### To build Armadillo
-To build run following command in the github root:
+Run following command in the github root:
 ```./gradlew build```
 
 To execute in 'dev' run following command in the github root:
 ```./gradlew run```
 
 ### Setting up development tools
-
 This repository uses `pre-commit` to manage commit hooks. An installation guide can be found
-[here](https://pre-commit.com/index.html#1-install-pre-commit). To install the hooks, run `pre-commit install` once in the root folder of this repository. Now
+[here](https://pre-commit.com/index.html#1-install-pre-commit). To install the hooks, run `pre-commit install` from the root folder of this repository. Now
 your code will be automatically formatted whenever you commit.
 
 ### How to change data directory
-
 Data is automatically stored in the `data` folder in this repository. You can choose another location
 in `application.yml` by changing the `storage.root-dir`
 setting.
 
 > **_Note_**: When you run Armadillo locally for the first time, the `lifecycle` project has not been
 > added to the system metadata yet. To add it automatically, see [Application properties](#application-properties).
-> Or you can add it manually:
+> Alternatively you can add it manually:
 > - Go to the Swagger UI (`http://localhost:8080/swagger-ui/index.html`)
 > - Go to the `PUT /access/projects` endpoint
 > - Add the project `lifecycle`
@@ -57,7 +53,7 @@ setting.
 
 ### Working with resources in development mode
 When developing locally, docker has trouble connecting to localhost. This problem becomes clear when working with
-resources. Luckily there's a quick fix for the problem. Instead of defining a resource as for example
+resources. Luckily there is a quick fix for the problem. Instead of defining a resource as for example
 `http://localhost:8080/storage/projects/omics/objects/test%2Fgse66351_1.rda`, rewrite it to:
 `http://host.docker.internal:8080/storage/projects/omics/objects/test%2Fgse66351_1.rda`. Here's some example R code
 for uploading resources:

docs/ops/configuring.md

@@ -13,14 +13,9 @@ connected institutions, ideally using a federated AAI such as LifeScience AAI.
 
 ### Configure DataSHIELD profiles
 To analyse data, users must choose a datashield profile. Armadillo owners can use the web user interface to configure new profiles. Assuming you
-installed docker you can also start/stop these images. Alternatively you can use docker-compose for that.
-
-There are DataSHIELD packages for [standard statistical analysis](https://github.com/datashield/dsBaseClient)
-, [exposome studies](https://github.com/isglobal-brge/dsExposomeClient)
-, [survival studies](https://github.com/neelsoumya/dsSurvivalClient)
-, [microbiome studies](https://github.com/StuartWheater/dsMicrobiomeClient)
-and [analysis tools for studies that are using large genetic datasets](https://github.com/isglobal-brge/dsomicsclient)
-. These packages can all be installed in the Armadillo suite.
+installed docker you can also start/stop these images. Alternatively you can use docker-compose for that. We
+recommend selecting one of the
+[DataSHIELD standard profiles](https://www.datashield.org/help/standard-profiles-and-plaforms).
 
 ### End users can use Armadillo as any other DataSHIELD server
 A researcher connects from an [R client](https://molgenis.github.io/molgenis-r-datashield) to one or multiple Armadillo servers. The data is

docs/ops/install/install_apache.md

@@ -1,10 +1,6 @@
 # Apache
 
-> We do however not provide any support regarding this configuration.
-
-It is possible to run Molgenis Armadillo using Apache.
-
-Below are some hints found.
+It is possible to run Molgenis Armadillo using Apache, however we do not provide support with this configuration.
 
 ## Encoding
 
@@ -14,8 +10,6 @@ Apache requires some additional configuration to get the `/storage/projects/{pro
 - subsets cannot be created
 - resources cannot be used.
 
-This basically means Armadillo is not usable. 
-
 ## Tell Armadillo about https
 
 We need to tell Armadillo server how to building URLs.

docs/ops/install/install_docker.md

@@ -6,5 +6,5 @@ For testing without having to installing Java you can run using docker:
 3. Execute ```docker-compose up```
 4. Once it says 'Started' go to http://localhost:8080 to see your Armadillo running.
 
-The command must run in same directory as downloaded docker file. We made docker available via 'docker.sock' so we can start/stop DataSHIELD profiles. Alternatively you must include the datashield profiles into this docker-compose. You can override all application.yaml settings via environment variables 
+The command must run in the same directory as the downloaded docker file. We made docker available via 'docker.sock' so we can start/stop DataSHIELD profiles. Alternatively you must include the datashield profiles into this docker-compose. You can override all application.yaml settings via environment variables 
 (see commented code in docker-compose file).

docs/release-test.md

@@ -1,8 +1,8 @@
 # Release testing
 ## Prerequisites
-- Testserver with release candidate available
+- Test server with release candidate available
 - OIDC user with admin permissions on testserver
-- Following libraries installed in R:
+- The following libraries installed in R:
   - cli
   - getPass
   - arrow