diff --git a/.circleci/config.yml b/.circleci/config.yml index 73a3446b9..21a0407c8 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -7,7 +7,7 @@ version: 2.1 jobs: build: docker: - - image: eclipse-temurin:17.0.8_7-jdk-jammy + - image: eclipse-temurin:17.0.9_9-jdk-jammy working_directory: ~/repo resource_class: large diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 000000000..ebee4b918 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,63 @@ +# Contributing to Armadillo + +## Running Armadillo from source code + +You can run from source code as follows: + +1. Install Java and Docker +2. Checkout the source using ```git clone https://github.com/molgenis/molgenis-service-armadillo.git``` +3. Optionally copy ```application.template.yml``` to ```application.yml``` to change settings (will be .gitignored) +4. Compile and execute the code using ```./gradlew run``` + +Note: contact MOLGENIS team if you want to contribute and need a testing OIDC config that you can run against localhost. + +# Developing Armadillo + +We use gradle to build: +* run using ```./gradlew run``` +* run tests using ```./gradlew test``` + +We use intellij to develop +* To run or debug in intellij, right click on armadillo/src/main/java/org.molgenis.armdadillo/ArmadilloServiceAppliction and choose 'Run/Debug Armadillo...' +* To run using oidc, create a copy of [application.yml](application.template.yml) in root of your project + +We have a swagger-ui to quickly see and test available web services at http://localhost:8080/swagger-ui/ + +## Profile xenon with resourcer whitelisted returns a host.docker.internal error +When developing locally, it might be possible to come across the container error: `Could not resolve host: host.docker.internal`, +especially when developing on a non-supported operating system when resourcer is whitelisted (such as xenon). +Sadly, the only way around this error is to edit the JAVA source code of Armadillo to include starting with an extra host. +To enable this feature, you must edit the private method `installImage` of [DockerService.java](https://github.com/molgenis/molgenis-service-armadillo/blob/master/armadillo/src/main/java/org/molgenis/armadillo/profile/DockerService.java) `CreateContainerCmd cmd` from `.withHostConfig(new HostConfig().withPortBindings(portBindings))` to `.withHostConfig(new HostConfig().withPortBindings(portBindings).withExtraHosts("host.docker.internal:host-gateway"))`. + +Please note that in order for this change to work, you must use Intellij to run Armadillo or compile the new source code. +Also, if you already have a xenon container build and running, stop and remove that container. + +# Developing DataSHIELD packages in Armadillo +As package developer will want to push your new packages into a DataSHIELD profile + +* You can start Armadillo with defaults as described above; then use admin/admin as authentication +* to see what profile are available and has been selected: +``` +curl -u admin:admin http://localhost:8080/profiles +``` +* to change selected profile 'my-profile': +``` +curl -X POST http://localhost:8080/select-profile \ + -H 'Content-Type: application/json' \ + -d 'default' +``` +* to install-packages in DataSHIELD current using admin user: +``` +curl -u admin:admin -v \ +-H 'Content-Type: multipart/form-data' \ +-F "file=@dsBase_6.3.0.tar.gz" \ +-X POST http://localhost:8080/install-package +``` +* to update whitelist of your current profile: +``` +curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase +``` +* to get whitelist of current profile: +``` +curl -u admin:admin http://localhost:8080/whitelist +``` diff --git a/Dockerfile b/Dockerfile index bde916396..807b33bee 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM eclipse-temurin:17.0.8_7-jdk-focal +FROM eclipse-temurin:17.0.9_9-jdk-focal VOLUME /data ARG JAR_FILE EXPOSE 8080 diff --git a/README.md b/README.md index 191507b3a..6b0ff7886 100644 --- a/README.md +++ b/README.md @@ -18,431 +18,8 @@ service provides the following features: ![DataSHIELD overview](https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/docs/img/overview-datashield.png) -# Armadillo installation -Armadillo requires Java to run, Docker to access the DataSHIELD profiles, and OIDC for authentication (not needed for local tests). Below instructions how to run Armadillo directly from Java, as a Docker container, as a service on Ubuntu or from source code. -Note that for production you should add a https proxy for essential security. And you might need to enable 'Docker socket' on your docker service. +## Getting started -### Run Armadillo using java commandline -Software developers often run Armadillo as java jar file: +For installing and using Armadillo see https://molgenis.github.io/molgenis-service-armadillo/#/ -1. Install Java and Docker (for the DataSHIELD profiles) -2. Download Armadillo jar file from [releases](https://github.com/molgenis/molgenis-service-armadillo/releases), for example: -[molgenis-armadillo-3.3.0.jar](https://github.com/molgenis/molgenis-service-armadillo/releases/download/V3.3.0/) -3. Run armadillo using ```java -jar molgenis-armadillo-3.3.0.jar``` -4. Go to http://localhost:8080 to see your Armadillo running. - -Default Armadillo will start with only 'basic-auth' and user 'admin' with password 'admin'. You can enable 'oidc' for connecting more users. You can change -by providing and editing [application.yaml](application.template.yml) file -in your working directory and then run command above again. - -### Run Armadillo via docker compose -For testing without having to installing Java you can run using docker: - -1. Install [docker-compose](https://docs.docker.com/compose/install/) -2. Download this [docker-compose.yml](docker-compose.yml). -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 -(see commented code in docker-compose file). - -### Run Armadillo as service on Ubuntu -We run Armadillo in production as a Linux service on Ubuntu, ensuring it gets restarted when the server is rebooted. You might be able to reproduce also on -CentOS (using yum instead of apt). - -#### 1. Install necessary software -``` -apt update -apt install openjdk-19-jre-headless -apt install docker.io -``` -Note: you might need 'sudo' - -#### 2. Run installation script -This step will install most recent [release](https://github.com/molgenis/molgenis-service-armadillo/releases): -``` -wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/scripts/install/armadillo-setup.sh -bash armadillo-setup.sh \ - --admin-user admin \ - --admin-password xxxxx - --domain my.server.com \ - --oidc \ - --oidc_url https://lifecycle-auth.molgenis.org \ - --oidc_clientid clientid \ - --oidc_clientsecret secret \ - --cleanup -``` -Note: adapt install command to suit your situation. Use --help to see the options. https://lifecycle-auth.molgenis.org is MOLGENIS provided OIDC service but -you can also use your own, see FAQ below. - -### Running Armadillo from source code - -You can run from source code as follows: -1. Install Java and Docker -2. Checkout the source using ```git clone https://github.com/molgenis/molgenis-service-armadillo.git``` -3. Optionally copy ```application.template.yml``` to ```application.yml``` to change settings (will be .gitignored) -4. Compile and execute the code using ```./gradlew run``` - -Note: contact MOLGENIS team if you want to contribute and need a testing OIDC config that you can run against localhost. - -# Using Armadillo -Armadillo has three main screens to manage projects, user access and DataSHIELD profiles: - -### Create data access projects -Data stewards can use the Armadillo web user interface or [MolgenisArmadillo R client](https://molgenis.github.io/molgenis-r-armadillo) -to create 'projects' and upload their data into those. Data tables need to be in parquet format that supports fast selections of the columns -(variables) you need for analysis. Other files can be configured as 'resources'. - -### Manage user access -Data stewards can use the permission screen to give email adresses access to the data. Everybody signs in via single sign on using an OIDC central -authentication server such as KeyCloack or Fusion auth that federates to authentication systems of -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. - -### 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 -loaded into an R session on the Armadillo server specifically created for the researcher. Analysis requests are sent to the R session on each Armadillo server. -There the analysis is performed and aggregated results are sent back to the client. - -# Developing Armadillo - -We use gradle to build: -* run using ```./gradlew run``` -* run tests using ```./gradlew test``` - -We use intellij to develop -* To run or debug in intellij, right click on armadillo/src/main/java/org.molgenis.armdadillo/ArmadilloServiceAppliction and choose 'Run/Debug Armadillo...' -* To run using oidc, create a copy of [application.yml](application.template.yml) in root of your project - -We have a swagger-ui to quickly see and test available web services at http://localhost:8080/swagger-ui/ - -# Developing DataSHIELD packages in Armadillo -As package developer will want to push your new packages into a DataSHIELD profile - -* You can start Armadillo with defaults as described above; then use admin/admin as authentication -* to see what profile are available and has been selected: -``` -curl -u admin:admin http://localhost:8080/profiles -``` -* to change selected profile 'my-profile': -``` -curl -X POST http://localhost:8080/select-profile \ - -H 'Content-Type: application/json' \ - -d 'default' -``` -* to install-packages in DataSHIELD current using admin user: -``` -curl -u admin:admin -v \ --H 'Content-Type: multipart/form-data' \ --F "file=@dsBase_6.3.0.tar.gz" \ --X POST http://localhost:8080/install-package -``` -* to update whitelist of your current profile: -``` -curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase -``` -* to get whitelist of current profile: -``` -curl -u admin:admin http://localhost:8080/whitelist -``` - -# Frequently asked questions - -### Docker gives a 'java.socket' error -You might need to enable Docker socket. On Docker desktop you can find that under 'settings' and 'advanced'. - -### Can I use docker compose to start profiles? -Instead of making Armadillo start/stop DataSHIELD profiles you can also use docker compose. -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? -Yes, you can run in 'offline' profile -``` -./gradlew run -Dspring.profiles.active=offline -``` - -### How to import data from Armadillo 2? -To export data from and Armadillo 2 server take the following steps: - -#### 1. Check if there's enough space left on the server -``` -du -h -``` -Compare to: -``` -du -h /var/lib/minio -``` -Available space should be at least twice the size of the MinIO folder. - -#### 2. Backup Armadillo 2 settings -``` -mkdir armadillo2-backup -rsync -avr /usr/share/armadillo armadillo2-backup -cp /etc/armadillo/application.yml armadillo2-backup/application-armadillo2.yml -``` -N.B.change /usr/share to path matching your local config. - -#### 3. Install helper software -Login to your server as root, using ssh. -``` -apt update -apt install pip -pip install minio -pip install fusionauth-client -pip install simple_term_menu -``` -If you get a purple message asking to update, accept and install everything. -Restart of server is recommended after this. - -N.B. Note that the commands in this manual are for Ubuntu, on other linux systems, -the `apt` command needs to be replaced with another one. - -#### 4. Stop all docker images for Armadillo 2 -List all docker images -```docker ps -a``` - -Stop and remove all Armadillo 2 related images (except for MinIO), e.g. -``` -docker rm armadillo_auth_1 armadillo_console_1 armadillo_rserver-default_1 armadillo_rserver-mediation_1 armadillo_rserver-exposome_1 armadillo_rserver-omics_1 armadillo_armadillo_1 -f -``` -Check with `docker ps -a` if there are still containers running, if so remove these (except for the MinIO) in the same way as the others. - -#### 5. Install armadillo -``` -apt update -apt install openjdk-19-jre-headless -apt install docker.io -``` -The docker.io step might fail because containerd already exists, if that's the case, remove containerd and try again: -``` -apt remove containerd -apt install docker.io -``` - -Get armadillo: -``` -wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/scripts/install/armadillo-setup.sh -bash armadillo-setup.sh \ - --admin-user admin \ - --admin-password xxxxx - --domain my.server.com \ - --oidc \ - --oidc_url https://lifecycle-auth.molgenis.org \ - --oidc_clientid clientid \ - --oidc_clientsecret secret \ - --cleanup \ -``` -Don't forget to set a proper admin password (use a generator), domain, clientid and clientsecret. The client id and -secret can be found on the lifecycle auth server in the configuration for your server. If you don't have permissions to -receive this, you can ask the support team to get it for you. - -Open armadillo in the browser and try to login using basicauth to check if the server is running properly. If it's not -running at all, try: -``` -systemctl start armadillo -``` - -#### 6. Export data from Armadillo 2 into armadillo 3 -Look up the user/password in the application.yml of the old armadillo. They're called MinIO access key and minio -secret key. -``` -cat /root/armadillo2-backup/application-armadillo2.yml -``` -Do the following step in a separate screen. On ubuntu use: -``` -screen -``` -Navigate to the armadillo folder: -``` -cd /usr/share/armadillo -``` -This step will copy Armadillo 2 data from minio into the folder matching of an Armadillo 3 data folder: -``` -mkdir data -wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/scripts/migrate-minio.py -python3 migrate-minio.py --minio http://localhost:9000 --target /usr/share/armadillo/data -``` - -This might take a couple of minutes. You can detach the screen using `ctrl+a` followed by `d` and reattach it using -`screen -r`. - -#### 7. Run Armadillo 3 using exported data -Make sure to move the exported data into the new 'data' folder. Optionally you might need to fix user permissions, e.g.: -``` -chown armadillo:armadillo -R data -``` -Check if armadillo is running by going to the URL of your server in the browser, login and navigate to the projects tab. - -#### 8. Optionally, acquire a permission set from MOLGENIS team -If you previously run central authorisation server with MOLGENIS team, they can provide you with procedure to load -pre-existing permissions. They will use: -``` -wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/scripts/migrate-auth.py -python3 migrate-auth.py --fusion-auth https://lifecycle-auth.molgenis.org --armadillo https://thearmadillourl.net -``` -Now check if all users and data are properly migrated. - -#### 9. Cleanup ngnix config - -Change `/etc/ngninx/sites-available/armadillo.conf` to: -``` -server { - listen 80; - server_name urlofyourserver.org - include /etc/nginx/global.d/*.conf; - location / { - proxy_pass http://localhost:8080; - client_max_body_size 0; - proxy_read_timeout 600s; - proxy_redirect http://localhost:8080/ $scheme://$host/; - proxy_set_header Host $host; - proxy_http_version 1.1; - } -} -``` -Note that the `https://` is missing in the server_name part. - -Remove the console and storage file from: `/etc/ngninx/sites-enabled/`. - -``` -system restart ngninx -``` - -#### 10. Fix application.yml -Make sure the following is added: -``` -server: -forward-headers-strategy: framework -``` - -#### 11. Fix URLs in the lifecycle FusionAuth -Add the following to the config of your server: -`https://yourserver.com/login/oauth2/code/molgenis` - -#### 12. Set up profiles -Login to armadillo in the browser. Navigate to the "Profiles" tab. Add a new profile with the following properties: - -Name: `xenon` -Image: `datashield/armadillo-rserver_caravan-xenon:latest` -Package whitelist: `dsBase`, `resourcer`, `dsMediation`, `dsMTLBase`, `dsSurvival`, `dsExposome` - -Assign a random 9-number seed and create and start the container. - -#### 13. Remove old MinIO data -First remove the MinIO docker container. First check the name of the container using `docker ps -a`, then: -``` -docker rm containername -f -``` -After that remove the data: -```rm -Rf /var/lib/minio/ ``` - - -### How to run previous armadillo 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: -```./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 -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: -> - Go to the Swagger UI (`http://localhost:8080/swagger-ui/index.html`) -> - Go to the `PUT /access/projects` endpoint -> - Add the project `lifecycle` -> -> Now you're all set! - -#### 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 -`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: -```R -## Uploading resources -library(MolgenisArmadillo) -library(resourcer) - -token <- armadillo.get_token("http://localhost:8080/") - -resGSE1 <- resourcer::newResource( - name = "GSE66351_1", - secret = token, - url = "http://host.docker.internal:8080/storage/projects/omics/objects/test%2Fgse66351_1.rda", - format = "ExpressionSet" -) - -armadillo.login("http://localhost:8080/") -armadillo.upload_resource(project="omics", folder="ewas", resource = resGSE1, name = "GSE66351_1") -``` -And for using them: -```R -library(DSMolgenisArmadillo) -library(dsBaseClient) - -token <- armadillo.get_token("http://localhost:8080/") - -builder <- DSI::newDSLoginBuilder() -builder$append( - server = "local", - url = "http://localhost:8080/", - token = token, - driver = "ArmadilloDriver", - profile = "uniform", - resource = "omics/ewas/GSE66351_1" -) - -login_data <- builder$build() -conns <- DSI::datashield.login(logins = login_data, assign = TRUE) - -datashield.resources(conns = conns) -datashield.assign.resource(conns, resource="omics/ewas/GSE66351_1", symbol="eSet_0y_EUR") -ds.class('eSet_0y_EUR', datasources = conns) -datashield.assign.expr(conns, symbol = "methy_0y_EUR",expr = quote(as.resource.object(eSet_0y_EUR))) -``` - -### Profile xenon with resourcer whitelisted returns a host.docker.internal error -When developing locally, it might be possible to come across the container error: `Could not resolve host: host.docker.internal`, -especially when developing on a non-supported operating system when resourcer is whitelisted (such as xenon). -Sadly, the only way around this error is to edit the JAVA source code of Armadillo to include starting with an extra host. -To enable this feature, you must edit the private method `installImage` of [DockerService.java](https://github.com/molgenis/molgenis-service-armadillo/blob/master/armadillo/src/main/java/org/molgenis/armadillo/profile/DockerService.java) `CreateContainerCmd cmd` from `.withHostConfig(new HostConfig().withPortBindings(portBindings))` to `.withHostConfig(new HostConfig().withPortBindings(portBindings).withExtraHosts("host.docker.internal:host-gateway"))`. - -Please note that in order for this change to work, you must use Intellij to run Armadillo or compile the new source code. -Also, if you already have a xenon container build and running, stop and remove that container. +For developing and contributing see [Contributing](./CONTRIBUTING.md). diff --git a/armadillo/build.gradle b/armadillo/build.gradle index fe0918e87..bb5d1e0ac 100644 --- a/armadillo/build.gradle +++ b/armadillo/build.gradle @@ -44,7 +44,7 @@ dependencies { //other implementation 'org.rosuda.REngine:REngine:2.1.0' implementation 'org.rosuda.REngine:Rserve:1.8.1' - implementation 'io.swagger.core.v3:swagger-annotations:2.2.15' + implementation 'io.swagger.core.v3:swagger-annotations:2.2.19' implementation 'com.google.auto.value:auto-value-annotations:1.10.4' implementation 'org.obiba.datashield:ds4j-core:2.0.0' implementation 'org.obiba.datashield:ds4j-r:2.0.0' diff --git a/armadillo/src/main/java/org/molgenis/armadillo/controller/StorageController.java b/armadillo/src/main/java/org/molgenis/armadillo/controller/StorageController.java index da5a38d0c..aea0277e7 100644 --- a/armadillo/src/main/java/org/molgenis/armadillo/controller/StorageController.java +++ b/armadillo/src/main/java/org/molgenis/armadillo/controller/StorageController.java @@ -5,7 +5,6 @@ import static org.springframework.http.HttpStatus.OK; import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE; import static org.springframework.http.MediaType.APPLICATION_OCTET_STREAM; -import static org.springframework.http.MediaType.APPLICATION_OCTET_STREAM_VALUE; import static org.springframework.http.MediaType.MULTIPART_FORM_DATA_VALUE; import static org.springframework.http.ResponseEntity.noContent; import static org.springframework.http.ResponseEntity.notFound; @@ -27,13 +26,12 @@ import java.util.Map; import org.molgenis.armadillo.audit.AuditEventPublisher; import org.molgenis.armadillo.exceptions.FileProcessingException; +import org.molgenis.armadillo.exceptions.UnknownObjectException; +import org.molgenis.armadillo.exceptions.UnknownProjectException; import org.molgenis.armadillo.storage.ArmadilloStorageService; import org.molgenis.armadillo.storage.FileInfo; import org.springframework.core.io.InputStreamResource; -import org.springframework.http.ContentDisposition; -import org.springframework.http.HttpHeaders; -import org.springframework.http.HttpStatus; -import org.springframework.http.ResponseEntity; +import org.springframework.http.*; import org.springframework.security.access.prepost.PreAuthorize; import org.springframework.web.bind.annotation.DeleteMapping; import org.springframework.web.bind.annotation.GetMapping; @@ -46,6 +44,7 @@ import org.springframework.web.bind.annotation.ResponseStatus; import org.springframework.web.bind.annotation.RestController; import org.springframework.web.multipart.MultipartFile; +import org.springframework.web.server.ResponseStatusException; @Tag(name = "storage", description = "API to manipulate the storage") @RestController @@ -252,35 +251,38 @@ public void deleteObject( @PreAuthorize("hasAnyRole('ROLE_SU', 'ROLE_' + #project.toUpperCase() + '_RESEARCHER')") @ApiResponses( value = { - @ApiResponse(responseCode = "204", description = "Object downloaded successfully"), + @ApiResponse(responseCode = "200", description = "Object downloaded successfully"), @ApiResponse( responseCode = "404", description = "Unknown project or object", - content = @Content(schema = @Schema(hidden = true))), + content = @Content(mediaType = "application/json")), @ApiResponse( responseCode = "401", description = "Unauthorized", - content = @Content(schema = @Schema(hidden = true))) + content = @Content(mediaType = "application/json")) }) - @GetMapping( - value = "/projects/{project}/objects/{object}", - produces = {APPLICATION_OCTET_STREAM_VALUE}) - public @ResponseBody ResponseEntity downloadObject( + @GetMapping(value = "/projects/{project}/objects/{object}") + public ResponseEntity downloadObject( Principal principal, @PathVariable String project, @PathVariable String object) { - return auditor.audit( - () -> getObject(project, object), - principal, - DOWNLOAD_OBJECT, - Map.of(PROJECT, project, OBJECT, object)); + try { + return auditor.audit( + () -> getObject(project, object), + principal, + DOWNLOAD_OBJECT, + Map.of(PROJECT, project, OBJECT, object)); + } catch (UnknownObjectException | UnknownProjectException e) { + throw new ResponseStatusException(HttpStatus.NOT_FOUND, e.getMessage()); + } catch (Exception e) { + throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, e.getMessage()); + } } @PreAuthorize("hasAnyRole('ROLE_SU', 'ROLE_' + #project.toUpperCase() + '_RESEARCHER')") private ResponseEntity getObject(String project, String object) { - var inputStream = storage.loadObject(project, object); - var objectParts = object.split("/"); - var fileName = objectParts[objectParts.length - 1]; - try { + var inputStream = storage.loadObject(project, object); + var objectParts = object.split("/"); + var fileName = objectParts[objectParts.length - 1]; InputStreamResource inputStreamResource = new InputStreamResource(inputStream); ContentDisposition contentDisposition = ContentDisposition.attachment().filename(fileName).build(); @@ -291,7 +293,7 @@ private ResponseEntity getObject(String project, String obj httpHeaders.setContentDisposition(contentDisposition); httpHeaders.setContentLength(fileSize); httpHeaders.setContentType(APPLICATION_OCTET_STREAM); - return new ResponseEntity(inputStreamResource, httpHeaders, HttpStatus.OK); + return new ResponseEntity<>(inputStreamResource, httpHeaders, HttpStatus.OK); } catch (IOException e) { throw new FileProcessingException(); } diff --git a/build.gradle b/build.gradle index cf382ace3..1c036cdf7 100644 --- a/build.gradle +++ b/build.gradle @@ -1,5 +1,5 @@ plugins { - id 'org.springframework.boot' version '3.1.2' + id 'org.springframework.boot' version '3.1.5' id "io.spring.dependency-management" version "1.1.3" id "java" id "org.sonarqube" version "3.5.0.2730" diff --git a/docs/README.md b/docs/README.md index 621b105dc..c6d0b840a 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1 +1,13 @@ -See /README.md \ No newline at end of file +# Overview + +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 + '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. +* **configure DataSHIELD analysis profiles**. [DataSHIELD analysis profiles](https://www.datashield.org/help/standard-profiles-and-plaforms) are + Docker images that contain a collection of multiple [DataSHIELD analysis packages](https://www.datashield.org/help/community-packages). + +![DataSHIELD overview](https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/docs/img/overview-datashield.png) + diff --git a/docs/_navbar.md b/docs/_navbar.md index 09fbae6ac..12b325e9c 100644 --- a/docs/_navbar.md +++ b/docs/_navbar.md @@ -16,4 +16,6 @@ * [ds-dictionaries](https://github.com/lifecycle-project/ds-dictionaries/blob/master/README.md) - * [Armadillo 2 to 3 migration guide](/migration-guide-2-to-3.md#instructions-for-migrating-a-2x-armadillo-to-3x "Armadillo 2 to 3 migration guide") \ No newline at end of file + * [Migration from 2 to 3](/upgrade-2-3.md) + + * [Release test (R)](/release-test.md) diff --git a/docs/_sidebar.md b/docs/_sidebar.md index 0a5ab0aba..abbc11d08 100644 --- a/docs/_sidebar.md +++ b/docs/_sidebar.md @@ -1,17 +1,14 @@ - [Armadillo suite](/ "Armadillo suite") - -- [Armadillo 3 UI](/ui.md#armadillo-user-interface "Armadillo 3 UI") - -- [DsMolgenisArmadillo](https://github.com/molgenis/molgenis-r-datashield/blob/master/README.md) - -- [MolgenisArmadillo](https://molgenis.github.io/molgenis-r-armadillo/) - -- [molgenis-r-auth](https://molgenis.github.io/molgenis-r-auth/) - -- [molgenis-r-client](https://github.com/molgenis/molgenis-r-client/blob/master/README.md) - -- [ds-upload](https://lifecycle-project.github.io/ds-upload/) - -- [ds-dictionaries](https://github.com/lifecycle-project/ds-dictionaries/blob/master/README.md) - -- [Armadillo 2 to 3 migration guide](/migration-guide-2-to-3.md#instructions-for-migrating-a-2x-armadillo-to-3x "Armadillo 2 to 3 migration guide") \ No newline at end of file + - [Install](/ops/installing.md) + - [Configure](/ops/configuring.md) + - [UI](/ui.md#armadillo-user-interface "Armadillo 3 UI") + - [FAQ](/faq.md) + - [Migration from 2 to 3](/upgrade-2-3.md) + - [Release test (R)](/release-test.md) +- External sites + - [DsMolgenisArmadillo](https://github.com/molgenis/molgenis-r-datashield/blob/master/README.md) + - [MolgenisArmadillo](https://molgenis.github.io/molgenis-r-armadillo/) + - [molgenis-r-auth](https://molgenis.github.io/molgenis-r-auth/) + - [molgenis-r-client](https://github.com/molgenis/molgenis-r-client/blob/master/README.md) + - [ds-upload](https://lifecycle-project.github.io/ds-upload/) + - [ds-dictionaries](https://github.com/lifecycle-project/ds-dictionaries/blob/master/README.md) diff --git a/docs/faq.md b/docs/faq.md new file mode 100644 index 000000000..bcde8f572 --- /dev/null +++ b/docs/faq.md @@ -0,0 +1,105 @@ +# Frequently asked questions + +## Docker gives a 'java.socket' error +You might need to enable Docker socket. On Docker desktop you can find that under 'settings' and 'advanced'. + +## Can I use docker compose to start profiles? +Instead of making Armadillo start/stop DataSHIELD profiles you can also use docker compose. +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? +Yes, you can run in 'offline' profile +``` +./gradlew run -Dspring.profiles.active=offline +``` + +## How to run previous armadillo 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: +```./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 +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: +> - Go to the Swagger UI (`http://localhost:8080/swagger-ui/index.html`) +> - Go to the `PUT /access/projects` endpoint +> - Add the project `lifecycle` +> +> Now you're all set! + +### 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 +`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: +```R +## Uploading resources +library(MolgenisArmadillo) +library(resourcer) + +token <- armadillo.get_token("http://localhost:8080/") + +resGSE1 <- resourcer::newResource( + name = "GSE66351_1", + secret = token, + url = "http://host.docker.internal:8080/storage/projects/omics/objects/test%2Fgse66351_1.rda", + format = "ExpressionSet" +) + +armadillo.login("http://localhost:8080/") +armadillo.upload_resource(project="omics", folder="ewas", resource = resGSE1, name = "GSE66351_1") +``` +And for using them: +```R +library(DSMolgenisArmadillo) +library(dsBaseClient) + +token <- armadillo.get_token("http://localhost:8080/") + +builder <- DSI::newDSLoginBuilder() +builder$append( + server = "local", + url = "http://localhost:8080/", + token = token, + driver = "ArmadilloDriver", + profile = "uniform", + resource = "omics/ewas/GSE66351_1" +) + +login_data <- builder$build() +conns <- DSI::datashield.login(logins = login_data, assign = TRUE) + +datashield.resources(conns = conns) +datashield.assign.resource(conns, resource="omics/ewas/GSE66351_1", symbol="eSet_0y_EUR") +ds.class('eSet_0y_EUR', datasources = conns) +datashield.assign.expr(conns, symbol = "methy_0y_EUR",expr = quote(as.resource.object(eSet_0y_EUR))) +``` diff --git a/docs/migration-guide-2-to-3.md b/docs/migration-guide-2-to-3.md deleted file mode 100644 index 646081388..000000000 --- a/docs/migration-guide-2-to-3.md +++ /dev/null @@ -1,138 +0,0 @@ -# Instructions for migrating a 2.x Armadillo to 3.x -The release of Armadillo 3.0 introduces some breaking changes. These instructions will guide you -through the steps needed to migrate your old Armadillo service to the new version. - -## Configuration -This section is about changes in the `application.yml` configuration file. For a full -example you can look at [the application.yml in the code](/armadillo/src/main/resources/application.yml). - -### OIDC -Besides accepting JWTs from a trusted authentication provider, you can now enable OIDC authentication. -This will make it possible for admins to log in with their institute account in the UI. - -To enable this, add the following properties: - -``` -spring: - security: - oauth2: - client: - registration: - molgenis: - client-id: - client-secret: -``` - -### Armadillo Settings -The `datashield` property has been renamed to `armadillo`, and some new settings have been -introduced: - -``` -armadillo: - oidc-permission-enabled: false - oidc-admin-user: user@yourinstitute.org - docker-management-enabled: true -``` - -These settings are explained in more detail below. - -#### OIDC Permission Enabled -By default, roles and permissions are managed in Armadillo itself. However, you can still accept -roles from your authentication provider by setting `oidc-permission-enabled` to `true`. This is -not recommended. - -#### OIDC Admin User -You can configure a default OIDC admin user by setting the `oidc-admin-user` property. Armadillo -will add this user when the application starts. This admin will then immediately be able to login -with their institute account. - -#### Docker Management Enabled -Armadillo can manage the Docker containers used for profiles. To enable, set `docker-management-enabled` -to `true`. Keep in mind that Armadillo needs to be able to access a local Docker instance. - -### Profiles -Profiles can now be created and managed at runtime in the UI or via the profiles API. However, -it is still possible to configure one or more profiles, which will be created for you when -the application starts. - -Before 3.0, profiles and R environments had to be defined separately: - -``` -rserve: - environments: - - name: default - host: localhost - port: 6311 - -datashield: - profiles: - - name: default - environment: default - whitelist: - - dsBase - options: - datashield: - seed: 342325352 -``` - -This is no longer the case. You now have to configure everything inside a profile: - -``` -armadillo: - profiles: - - name: default - image: datashield/armadillo-rserver - host: localhost - port: 6311 - whitelist: - - dsBase - options: - datashield: - seed: 342325352 -``` - -Note that the root `datashield` property has been renamed to `armadillo`. - -Also note the `image` property: this one is optional and only necessary when you have enabled -[Docker Management](#docker-management). The image should be an image available on DockerHub. - -### Storage -You can now choose where Armadillo should store data: on a MinIO server (like before) or on the local file system. - -If you want to keep using MinIO, you don't need to change anything. The old configuration will still work: - -``` -minio: - url: http://localhost - port: 9000 - access-key: - secret-key: -``` - -To use the local file system, set the following parameter: - -``` -storage: - root-dir: -``` - -MinIO has precedence over local file storage, so keep that in mind when you have both configured. - -## Migrating users and data - -Since users and permissions are now managed in Armadillo instead of the authentication server, this -information needs to be migrated. And if you choose to host the data on the local file system -instead of a MinIO server, the data needs to be migrated as well. For both scenarios we have migration -scripts. - -### User migration script: Fusion Auth to Armadillo -To migrate users from Fusion Auth to Armadillo, you can use the script found [here](/scripts/migrate-auth.py). -More information on how to run it can be found in the script or by calling it with the `-h` flag. Make -sure Armadillo is NOT running when you run the script. After the script is done you need to start -Armadillo and it will automatically create the projects based on the folders that were copied. - -### Data migration script: MinIO to local file system -To migrate data from MinIO to the local file system, you can use the script found [here](/scripts/migrate-minio.py). -More information on how to run it can be found in the script or by calling it with the `-h` flag. Make -sure Armadillo is running when you run the script. - diff --git a/docs/ops/configuring.md b/docs/ops/configuring.md new file mode 100644 index 000000000..331669e03 --- /dev/null +++ b/docs/ops/configuring.md @@ -0,0 +1,28 @@ +# Using Armadillo +Armadillo has three main screens to manage projects, user access and DataSHIELD profiles: + +### Create data access projects +Data stewards can use the Armadillo web user interface or [MolgenisArmadillo R client](https://molgenis.github.io/molgenis-r-armadillo) +to create 'projects' and upload their data into those. Data tables need to be in parquet format that supports fast selections of the columns +(variables) you need for analysis. Other files can be configured as 'resources'. + +### Manage user access +Data stewards can use the permission screen to give email adresses access to the data. Everybody signs in via single sign on using an OIDC central +authentication server such as KeyCloack or Fusion auth that federates to authentication systems of +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. + +### 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 +loaded into an R session on the Armadillo server specifically created for the researcher. Analysis requests are sent to the R session on each Armadillo server. +There the analysis is performed and aggregated results are sent back to the client. diff --git a/docs/ops/installing.md b/docs/ops/installing.md new file mode 100644 index 000000000..1e492a19d --- /dev/null +++ b/docs/ops/installing.md @@ -0,0 +1,56 @@ +# Armadillo installation +Armadillo requires Java to run, Docker to access the DataSHIELD profiles, and OIDC for authentication (not needed for local tests). Below instructions how to run Armadillo directly from Java, as a Docker container, as a service on Ubuntu or from source code. +Note that for production you should add a https proxy for essential security. And you might need to enable 'Docker socket' on your docker service. + +## Run Armadillo using java commandline +Software developers often run Armadillo as java jar file: + +1. Install Java and Docker (for the DataSHIELD profiles) +2. Download Armadillo jar file from [releases](https://github.com/molgenis/molgenis-service-armadillo/releases), for example: +[molgenis-armadillo-3.3.0.jar](https://github.com/molgenis/molgenis-service-armadillo/releases/download/V3.3.0/) +3. Run armadillo using ```java -jar molgenis-armadillo-3.3.0.jar``` +4. Go to http://localhost:8080 to see your Armadillo running. + +Default Armadillo will start with only 'basic-auth' and user 'admin' with password 'admin'. You can enable 'oidc' for connecting more users. You can change +by providing and editing [application.yaml](application.template.yml) file +in your working directory and then run command above again. + +## Run Armadillo via docker compose +For testing without having to installing Java you can run using docker: + +1. Install [docker-compose](https://docs.docker.com/compose/install/) +2. Download this [docker-compose.yml](docker-compose.yml). +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 +(see commented code in docker-compose file). + +## Run Armadillo as service on Ubuntu +We run Armadillo in production as a Linux service on Ubuntu, ensuring it gets restarted when the server is rebooted. You might be able to reproduce also on +CentOS (using yum instead of apt). + +### 1. Install necessary software +``` +apt update +apt install openjdk-19-jre-headless +apt install docker.io +``` +Note: you might need 'sudo' + +### 2. Run installation script +This step will install most recent [release](https://github.com/molgenis/molgenis-service-armadillo/releases): +``` +wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/scripts/install/armadillo-setup.sh +bash armadillo-setup.sh \ + --admin-user admin \ + --admin-password xxxxx + --domain my.server.com \ + --oidc \ + --oidc_url https://lifecycle-auth.molgenis.org \ + --oidc_clientid clientid \ + --oidc_clientsecret secret \ + --cleanup +``` +Note: adapt install command to suit your situation. Use --help to see the options. https://lifecycle-auth.molgenis.org is MOLGENIS provided OIDC service but +you can also use your own, see FAQ below. diff --git a/docs/upgrade-2-3.md b/docs/upgrade-2-3.md new file mode 100644 index 000000000..e6b7fe097 --- /dev/null +++ b/docs/upgrade-2-3.md @@ -0,0 +1,178 @@ +### Migrate Armadillo 2 to Armadillo 3 + +To export data from and Armadillo 2 server take the following steps: + +#### 1. Check if there's enough space left on the server +``` +df -h +``` +Compare to: +``` +du -h /var/lib/minio +``` +Available space should be at least twice the size of the MinIO folder. + +#### 2. Backup Armadillo 2 settings +``` +mkdir armadillo2-backup +rsync -avr /usr/share/armadillo armadillo2-backup +cp /etc/armadillo/application.yml armadillo2-backup/application-armadillo2.yml +``` +N.B.change /usr/share to path matching your local config. + +#### 3. Install helper software +Login to your server as root, using ssh. +``` +apt update +apt install pip +pip install minio +pip install fusionauth-client +pip install simple_term_menu +``` +If you get a purple message asking to update, accept and install everything. +Restart of server is recommended after this. + +N.B. Note that the commands in this manual are for Ubuntu, on other linux systems, +the `apt` command needs to be replaced with another one. + +#### 4. Stop all docker images for Armadillo 2 +List all docker images +```docker ps -a``` + +Stop and remove all Armadillo 2 related images (except for MinIO), e.g. +``` +docker rm armadillo_auth_1 armadillo_console_1 armadillo_rserver-default_1 armadillo_rserver-mediation_1 armadillo_rserver-exposome_1 armadillo_rserver-omics_1 armadillo_armadillo_1 -f +``` +Check with `docker ps -a` if there are still containers running, if so remove these (except for the MinIO) in the same way as the others. + +#### 5. Install armadillo +``` +apt update +apt install openjdk-19-jre-headless +apt install docker.io +``` +The docker.io step might fail because containerd already exists, if that's the case, remove containerd and try again: +``` +apt remove containerd.io +apt install docker.io +``` + +Get armadillo: +``` +wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/scripts/install/armadillo-setup.sh +bash armadillo-setup.sh \ + --admin-user admin \ + --admin-password xxxxx + --domain my.server.com \ + --oidc \ + --oidc_url https://lifecycle-auth.molgenis.org \ + --oidc_clientid clientid \ + --oidc_clientsecret secret \ + --cleanup \ +``` +Don't forget to set a proper admin password (use a generator), domain, clientid and clientsecret. The client id and +secret can be found on the lifecycle auth server in the configuration for your server. If you don't have permissions to +receive this, you can ask the support team to get it for you. + +Open armadillo in the browser and try to login using basicauth to check if the server is running properly. If it's not +running at all, try: +``` +systemctl start armadillo +``` + +#### 6. Export data from Armadillo 2 into armadillo 3 +Look up the user/password in the application.yml of the old armadillo. They're called MinIO access key and minio +secret key. +``` +cat /root/armadillo2-backup/application-armadillo2.yml +``` +Do the following step in a separate screen. On ubuntu use: +``` +screen +``` +Navigate to the armadillo folder: +``` +cd /usr/share/armadillo +``` +This step will copy Armadillo 2 data from minio into the folder matching of an Armadillo 3 data folder: +``` +mkdir data +wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/scripts/migrate-minio.py +python3 migrate-minio.py --minio http://localhost:9000 --target /usr/share/armadillo/data +``` + +This might take a couple of minutes. You can detach the screen using `ctrl+a` followed by `d` and reattach it using +`screen -r`. + +#### 7. Run Armadillo 3 using exported data +Make sure to move the exported data into the new 'data' folder. Optionally you might need to fix user permissions, e.g.: +``` +chown armadillo:armadillo -R data +``` +Check if armadillo is running by going to the URL of your server in the browser, login and navigate to the projects tab. + +#### 8. Optionally, acquire a permission set from MOLGENIS team +If you previously run central authorisation server with MOLGENIS team, they can provide you with procedure to load +pre-existing permissions. They will use: +``` +wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/master/scripts/migrate-auth.py +python3 migrate-auth.py --fusion-auth https://lifecycle-auth.molgenis.org --armadillo https://thearmadillourl.net +``` +Now check if all users and data are properly migrated. + +NOTE: if the script fails with a timeout, try pinging the armadillo url and lifecycle auth url to see if they're reachable from the server. In case they are not, you could choose to export the users using the `export-users.py` script locally and then manually enter them into the system. + +#### 9. Cleanup ngnix config + +Change `/etc/nginx/sites-available/armadillo.conf` to: +``` +server { + listen 80; + server_name urlofyourserver.org + include /etc/nginx/global.d/*.conf; + location / { + proxy_pass http://localhost:8080; + client_max_body_size 0; + proxy_read_timeout 600s; + proxy_redirect http://localhost:8080/ $scheme://$host/; + proxy_set_header Host $host; + proxy_http_version 1.1; + } +} +``` +Note that the `https://` is missing in the server_name part. +NOTE: if port 443 and the SSL certificates are in the old config, you mind have to keep that part, so you shouldn't comment that out. Keep the listen and certificate lines, comment out the rest and paste the config above below the existing config. + +Remove the console, auth and storage file from: `/etc/nginx/sites-enabled/` and `/etc/nginx/sites-available/. + +``` +systemctl restart nginx +``` + +#### 10. Fix application.yml +Make sure the following is added: +``` +server: +forward-headers-strategy: framework +``` + +#### 11. Fix URLs in the lifecycle FusionAuth +Add the following to the config of your server: +`https://yourserver.com/login/oauth2/code/molgenis` + +#### 12. Set up profiles +Login to armadillo in the browser. Navigate to the "Profiles" tab. Add a new profile with the following properties: + +Name: `xenon` +Image: `datashield/armadillo-rserver_caravan-xenon:latest` +Package whitelist: `dsBase`, `resourcer`, `dsMediation`, `dsMTLBase`, `dsSurvival`, `dsExposome` + +Assign a random 9-number seed and create and start the container. + +#### 13. Remove old MinIO data +First remove the MinIO docker container. First check the name of the container using `docker ps -a`, then: +``` +docker rm containername -f +``` +After that remove the data: +```rm -Rf /var/lib/minio/ ``` diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 4e86b9270..b1624c473 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,6 +1,6 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.2-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.3-bin.zip networkTimeout=10000 zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/scripts/ops/README.md b/scripts/ops/README.md index 96356c733..a54e08bc1 100644 --- a/scripts/ops/README.md +++ b/scripts/ops/README.md @@ -12,27 +12,29 @@ To make this possible Armadillo must have an admin user set. The file [`env.dist`](./env.dist) lists the required environment variables. -- Copy this over to a location of choice ie `conf/armadillo.acc.env` +- Copy this over to a location of choice ie `/etc/armadillo/acc.env` ### run -Make sure to `source` the file in your current `zsh` or through a new shell. +Make sure to `source` the file in your current `bash` or through a new shell. -```zsh -zsh -c "source conf/armadillo.acc.env ; ./armadilloctl.zsh" +```bash +bash -c "source /etc/armadillo/acc.env ; ./armadilloctl.bash" ``` ### examples -- `./armadillo.zsh statusAll` -- `./armadillo.zsh autoStart` -- `./armadillo.zsh stop default` -- `./armadillo.zsh startAll` +- `./armadillo.bash statusAll` +- `./armadillo.bash autoStart` +- `./armadillo.bash stop default` +- `./armadillo.bash startAll` ### Test script (WIP) -You can test `armadilloctl.zsh` using `test_armadilloctl.zsh`. +You can test `armadilloctl.bash` using `test_armadilloctl.bash`. -```zsh -zsh -c "source dev.env ; ./test_armadilloctl.zsh" || echo FAILED -``` +We source the environment variables to not contaminate our current shell. + +```bash +bash -c "source /etc/armadillo/acc.env ; ./test_armadilloctl.bash" || echo FAILED +``` \ No newline at end of file diff --git a/scripts/ops/armadilloctl.bash b/scripts/ops/armadilloctl.bash new file mode 100755 index 000000000..750ddb5cf --- /dev/null +++ b/scripts/ops/armadilloctl.bash @@ -0,0 +1,184 @@ +#!/usr/bin/env bash + +CURL_OPTS=--silent + +OK="\033[32m" +WARN="\033[33m" +ERR="\033[31m" +B="\033[0m" + +success() { + echo -e "${OK}${1}${B}" +} + +warning() { + echo -e "WARNING: ${WARN}${1}${B}" +} + +error() { + echo -e "ERROR: ${ERR}${1}${B}" + exit 1 +} + +is_armadillo_running() { + cmd="${ARMADILLO_URL}" + curl $CURL_OPTS --request "GET" "${cmd}" > /dev/null || (error "Armadillo not running."; exit 1) +} + +get_profiles() { + cmd="$ARMADILLO_URL/ds-profiles" + profile_names=$(curl $CURL_OPTS --user "${CREDENTIALS}" --request "GET" --header "accept: application/json" "${cmd}" | jq -r '.[] | "\(.name)"') +} + +status() { + if [ -z "$1" ]; then + error "$0 needs profile name. Or try ${0}All" + fi + name=$1 + + cmd="${ARMADILLO_URL}/ds-profiles/{$name}" + stats=$(curl $CURL_OPTS --user "${CREDENTIALS}" --request "GET" --header "accept: application/json" "${cmd}" | jq -r '"\(.name) = \(.container.status)"') + success "$stats" +} + +start() { + if [ -z "$1" ]; then + error "$0 needs profile name. Or try ${0}All" + fi + + profile="$1" + cmd="$ARMADILLO_URL/ds-profiles/$profile/start" + echo "Starting '$profile' on $cmd" + + curl $CURL_OPTS --user $CREDENTIALS --request "POST" "$cmd" --data "" +} + +stop() { + if [ -z "$1" ]; then + error "$0 needs profile name. Or try ${0}All" + fi + + profile="$1" + cmd="$ARMADILLO_URL/ds-profiles/$profile/stop" + echo "Stopping '$profile' on $cmd" + + curl $CURL_OPTS --user $CREDENTIALS --request "POST" $cmd --data "" +} + +restart() { + if [ -z "$1" ]; then + error "$0 needs profile name. Or try ${0}All" + fi + + profile=$1 + echo "Restarting $profile" + stop "$profile" + sleep 5 + start "$profile" + sleep 5 + status "$profile" + +} + +is_auto_start() { + if [[ $ARMADILLO_PROFILES_AUTOSTART =~ (^|[[:space:]])$1($|[[:space:]]) ]] + then + return 0 + else + return 1 + fi +} + +doAll() { + command=$1 + get_profiles + + echo "${profile_names}" | while read -r item; do + "$command" "${item}" + done +} + +statusAll() { + doAll status +} + +startAll() { + doAll start +} + +stopAll() { + doAll stop +} + +restartAll() { + doAll stop + sleep 5 + doAll start +} + +autoStart() { + get_profiles + echo "Auto starting ..." + echo "${profile_names}" | while read -r item + do + if is_auto_start "${item}" + then + start "${item}" + fi + done + statusAll +} + +check_dependencies() { + if ! which jq > /dev/null ; then + echo "Please install jq for json parsing ... exiting" + exit 1 + fi +} + +var_found() { + echo "Variable $1 found ..." +} + +var_empty() { + warning "Variable $1 not set! ... exiting" + exit 1 +} + +all_set() { + [[ -n "$ARMADILLO_URL" ]] && var_found ARMADILLO_URL + [[ -z "$ARMADILLO_URL" ]] && var_empty ARMADILLO_URL + + [[ -n "$ARMADILLO_ADMIN_USER" ]] && var_found ARMADILLO_ADMIN_USER + [[ -z "$ARMADILLO_ADMIN_USER" ]] && var_empty ARMADILLO_ADMIN_USER + + [[ -n "$ARMADILLO_ADMIN_PASSWORD" ]] && var_found ARMADILLO_ADMIN_PASSWORD + [[ -z "$ARMADILLO_ADMIN_PASSWORD" ]] && var_empty ARMADILLO_ADMIN_PASSWORD + + # Set to all if not set with value. + [[ -n "${ARMADILLO_PROFILES_AUTOSTART}" ]] && var_found ARMADILLO_PROFILES_AUTOSTART + [[ -z "${ARMADILLO_PROFILES_AUTOSTART}" ]] && ARMADILLO_PROFILES_AUTOSTART="__ALL__" + + CREDENTIALS="${ARMADILLO_ADMIN_USER}:${ARMADILLO_ADMIN_PASSWORD}" + + echo "" + echo "Armadillo settings:" + echo " ARMADILLO_URL : ${ARMADILLO_URL}" + echo " ARMADILLO_ADMIN_USER : ${ARMADILLO_ADMIN_USER}" + echo " ARMADILLO_PROFILES_AUTOSTART : ${ARMADILLO_PROFILES_AUTOSTART}" +} + +check_dependencies || exit + +all_set || exit + +is_armadillo_running || exit + +get_profiles + +if [[ "$1" =~ ^(status|start|stop|restart|statusAll|startAll|stopAll|restartAll|autoStart)$ ]]; then + "$@" +else + warning "Please provide one of the following arguments: status | start | stop | restart | statusAll | startAll | stopAll | restartAll | autoStart" + error "Got argument '$1'" +fi diff --git a/scripts/ops/env.dist b/scripts/ops/env.dist index 7b19ccef4..63cc264f3 100644 --- a/scripts/ops/env.dist +++ b/scripts/ops/env.dist @@ -1,11 +1,8 @@ # copy this file to ie "/etc/armadillo/acc.env" -# FIXME: We could / should test for admin user in overload config file instead? -# ARMADILLO_YML_FILE= - export ARMADILLO_URL=http://localhost:8080 export ARMADILLO_ADMIN_USER=admin export ARMADILLO_ADMIN_PASSWORD=admin # Space separated values between double quotes. Leaving empty falls back to all profiles. -export ARMADILLO_PROFILES_AUTOSTART="default rock" +export ARMADILLO_PROFILES_AUTOSTART="default rock" \ No newline at end of file diff --git a/scripts/ops/test_armadilloctl.bash b/scripts/ops/test_armadilloctl.bash new file mode 100755 index 000000000..03007166e --- /dev/null +++ b/scripts/ops/test_armadilloctl.bash @@ -0,0 +1,67 @@ +#!/usr/bin/env bash + +OUT=/dev/stdout +if [ -z "$1" ]; then + OUT="/dev/null" +fi + +usage() { + echo 'bash -c "source dev.env ; ./test_armadilloctl.bash" || echo FAILED' +} + +colors() { + for c in {0..255}; do + printf "\033[48;5;%sm%3d\033[0m " "$c" "$c" + if (( c == 15 )) || (( c > 15 )) && (( (c-15) % 6 == 0 )); then + printf "\n" + fi + done +} + +OK="\033[32m" +WARN="\033[33m" +ERR="\033[31m" +B="\033[0m" + +error() { + echo -e "TEST:: ERROR: ${ERR}${1}${B}" +} + +warning() { + echo -e "TEST:: WARNING: ${WARN}${1}${B}" +} + +success() { + echo -e "TEST:: SUCCES: ${OK}${1}${B}" +} + + +failed() { + warn $0 +} +do_sleep() { + warning "Pausing for $1 seconds before '$2'." + sleep "$1" + echo "..." +} + +error "NOTE: controller exit values are incomplete ... needs eyes" +warning "Make sure Armadillo is running" + +./armadilloctl.bash > $OUT || success "Needs a command." + +./armadilloctl.bash status > $OUT || success "status needs profile name" +./armadilloctl.bash statusAll > $OUT && success "statusAll needs running Armadillo" + +./armadilloctl.bash stopAll > $OUT && success "stopAll needs running Armadillo" + +do_sleep 5 "autoStart" +./armadilloctl.bash autoStart > $OUT && success "autoStart needs running Armadillo" + +do_sleep 5 "startAll" +./armadilloctl.bash startAll > $OUT && success "startAll needs running Armadillo" + +do_sleep 5 "restartAll" +./armadilloctl.bash restartAll > $OUT && success "restartAll needs running Armadillo" + +# colors diff --git a/scripts/release/dev.env.dist b/scripts/release/dev.env.dist index e4fe016cf..318edeb13 100644 --- a/scripts/release/dev.env.dist +++ b/scripts/release/dev.env.dist @@ -8,6 +8,9 @@ GIT_CLONE_PATH= # The RDA test file will also be placed in this path TEST_FILE_PATH= +# Do you want to manually test or automatic. Set to 'N' for non-interactive +INTERACTIVE=Y + PROFILE=xenon ARMADILLO_URL=http://localhost:8080 ADMIN_PASSWORD=admin diff --git a/scripts/release/release-test.R b/scripts/release/release-test.R index f97905b3c..8dbf30964 100755 --- a/scripts/release/release-test.R +++ b/scripts/release/release-test.R @@ -37,9 +37,6 @@ library(MolgenisArmadillo) library(DSI) library(dsBaseClient) -# FIXME: waiting for PR https://github.com/molgenis/molgenis-r-datashield/pull/62 -# needed for https://github.com/molgenis/molgenis-service-armadillo/pull/277 -#devtools::install("/Users/clemens/Documents/GitHub/molgenis-r-datashield/") library(DSMolgenisArmadillo) library(resourcer) @@ -169,8 +166,13 @@ set_user <- function(user, admin_pwd, isAdmin, project1, omics_project){ } wait_for_input <- function(){ - cat("\nPress any key to continue") - continue <- readLines("stdin", n=1) + if (interactive) { + cat("\nPress any key to continue") + continue <- readLines("stdin", n=1) + } + else { + cat("\n\n") + } } # log version info of loaded libraries @@ -468,6 +470,11 @@ if(armadillo_url == ""){ cli_alert_info(paste0("ARMADILLO_URL from '.env' file: ", armadillo_url)) } +interactive = TRUE +if (Sys.getenv("INTERACTIVE") == 'N') { + interactive = FALSE +} + armadillo_url <- add_slash_if_not_added(armadillo_url) if(url.exists(armadillo_url)) { @@ -700,11 +707,13 @@ wait_for_input() cat("\nVerify outcome contains nonrep and yearlyrep") wait_for_input() -cat("\nWere the manual tests successful? (y/n) ") -success <- readLines("stdin", n=1) -if(success != "y"){ - cli_alert_danger("Manual tests failed: problem in UI") - exit_test("Some values incorrect in UI projects view") +if (interactive) { + cat("\nWere the manual tests successful? (y/n) ") + success <- readLines("stdin", n=1) + if(success != "y"){ + cli_alert_danger("Manual tests failed: problem in UI") + exit_test("Some values incorrect in UI projects view") + } } cli_h2("Resource upload") @@ -714,9 +723,9 @@ cli_alert_info(sprintf("Creating project [%s]", omics_project)) armadillo.create_project(omics_project) rda_file_body <- upload_file(rda_dir) cli_alert_info(sprintf("Uploading resource file to %s into project [%s]", armadillo_url, omics_project)) - -post_resource_to_api(omics_project, token, auth_type, rda_file_body, "ewas", "gse66351_1.rda") - +system.time({ + post_resource_to_api(omics_project, token, auth_type, rda_file_body, "ewas", "gse66351_1.rda") +}) cli_alert_info("Creating resource") @@ -735,8 +744,11 @@ armadillo.upload_resource(project = omics_project, folder = "ewas", resource = r cli_alert_info("\nNow you're going to test as researcher") if(!ADMIN_MODE){ - cat("\nDo you want to remove admin from OIDC user automatically? (y/n) ") - update_auto <- readLines("stdin", n=1) + update_auto = "y" + if(interactive) { + cat("\nDo you want to remove admin from OIDC user automatically? (y/n) ") + update_auto <- readLines("stdin", n=1) + } if(update_auto == "y"){ set_user(user, admin_pwd, F, project1, omics_project) } @@ -750,24 +762,28 @@ if(!ADMIN_MODE){ } cli_h2("Using tables as researcher") + cli_alert_info("Creating new builder") cli_alert_info("Building") -logindata <- create_dsi_builder( - url = armadillo_url, - profile = profile, - password = admin_pwd, - token = token, - table = sprintf("%s/2_1-core-1_0/nonrep", project1) - ) - +logindata <- create_dsi_builder(url = armadillo_url, profile = profile, password = admin_pwd, token = token, table = sprintf("%s/2_1-core-1_0/nonrep", project1)) cli_alert_info(sprintf("Login with profile [%s] and table: [%s/2_1-core-1_0/nonrep]", profile, project1)) conns <- datashield.login(logins = logindata, symbol = "core_nonrep", variables = c("coh_country"), assign = TRUE) + cli_alert_info("Assigning table core_nonrep") datashield.assign.table(conns, "core_nonrep", sprintf("%s/2_1-core-1_0/nonrep", project1)) cli_alert_info("Assigning expression for core_nonrep$coh_country") datashield.assign.expr(conns, "x", expr=quote(core_nonrep$coh_country)) + cli_alert_info("Verifying connecting to profile possible") con <- create_ds_connection(password = admin_pwd, token = token, url=armadillo_url, profile=profile) +if (con@name == "armadillo") { + cli_alert_success("Succesfully connected") +} else { + # FIXME: should we exit? + cli_alert_danger("Connection failed") +} +dsDisconnect(con) + cli_alert_info("Verifying mean function works on core_nonrep$country") ds_mean <- ds.mean("core_nonrep$coh_country", datasources = conns)$Mean cli_alert_info("Verifying mean values") @@ -789,14 +805,18 @@ compare_list_values(hist$density, density) cli_alert_info("Validating histogram mids") compare_list_values(hist$mids, mids) +datashield.logout(conns) + if (ADMIN_MODE) { cli_alert_warning("Cannot test working with resources as basic authenticated admin") } else if (!"resourcer" %in% profile_info$packageWhitelist) { cli_alert_warning(sprintf("Resourcer not available for profile: %s, skipping testing using resources.", profile)) } else { cli_h2("Using resources as regular user") + login_data <- create_dsi_builder(server = "testserver", url = armadillo_url, token = token, profile = profile, resource = sprintf("%s/ewas/GSE66351_1", omics_project)) conns <- DSI::datashield.login(logins = login_data, assign = TRUE) + cli_alert_info("Testing if we see the resource") resource_path <- sprintf("%s/ewas/GSE66351_1", omics_project) if(datashield.resources(conns = conns)$testserver == resource_path){ @@ -820,6 +840,7 @@ if (ADMIN_MODE) { }, error = function(e) { cli_alert_danger(datashield.errors()) }) + datashield.logout(conns) } cli_h2("Default profile") @@ -830,16 +851,16 @@ if (con@name == "armadillo") { } else { cli_alert_danger("Connection failed") } +dsDisconnect(con) cli_alert_info("Verify if default profile works when specifying profile") - - con <- create_ds_connection(password = admin_pwd, token = token, url = armadillo_url, profile = "default") if (con@name == "armadillo") { cli_alert_success("Succesfully connected") } else { cli_alert_danger("Connection failed") } +dsDisconnect(con) cli_h2("Removing data as admin") cat("We're now continueing with the datamanager workflow as admin\n") @@ -925,14 +946,15 @@ datashield.assign.table(conns, "core_trimesterrep", sprintf("%s/core/trimesterre datashield.assign.expr(conns, "x", expr=quote(core_trimesterrep$smk_t)) con <- create_ds_connection(password = admin_pwd, token = token, profile = profile, url = armadillo_url) - if (con@name == "armadillo"){ cli_alert_success("Succesfully connected") } else { cli_alert_danger("Connection failed") } +dsDisconnect(con) ds_mean <- ds.mean("core_trimesterrep$smk_t", datasources = conns)$Mean +datashield.logout(conns) cli_alert_info("Testing Rock profile mean values") verify_ds_obtained_mean(ds_mean, 61.059, 3000) diff --git a/ui/build.gradle b/ui/build.gradle index eaab15c1b..c51c5e99c 100644 --- a/ui/build.gradle +++ b/ui/build.gradle @@ -36,10 +36,9 @@ task mybuild(type: YarnTask, dependsOn: yarn_install) { args = ['run', 'build'] } -//task runTest(type: YarnTask, dependsOn: mybuild) { -// args = ['run', 'test'] -//} -//test.dependsOn runTest +task test(type: YarnTask, dependsOn: mybuild) { + args = ['run', 'test'] +} /* convert build files into one apps.jar that we can use as a dependency in the java part */ task createJar(type: Zip, dependsOn: mybuild) { @@ -49,6 +48,7 @@ task createJar(type: Zip, dependsOn: mybuild) { from('dist') into('public') } +createJar.dependsOn test //first mybuild, than createJar build.dependsOn "createJar" diff --git a/ui/package.json b/ui/package.json index 8d82e1d02..ad9a75669 100644 --- a/ui/package.json +++ b/ui/package.json @@ -11,34 +11,29 @@ }, "dependencies": { "@popperjs/core": "2.11.8", - "bootstrap": "5.2.3", - "bootstrap-icons": "1.10.3", - "vue": "3.2.47", + "bootstrap": "5.3.2", + "bootstrap-icons": "1.11.1", + "vue": "3.3.8", "vue-router": "^4.0.13" }, "devDependencies": { - "@babel/preset-env": "^7.19.3", - "@babel/preset-typescript": "^7.18.6", - "@types/jest": "^29.1.1", - "@vitejs/plugin-vue": "4.1.0", - "@vue/test-utils": "^2.0.2", - "@vue/vue3-jest": "^29.1.1", - "babel-jest": "^29.1.2", - "cz-conventional-changelog": "3.3.0", - "jest": "^29.0.3", - "jest-environment-jsdom": "^29.1.2", - "jsdom": "^20.0.1", - "prettier": "2.8.8", - "sass": "1.60.0", - "ts-jest": "^29.0.3", - "ts-node": "^10.9.1", - "tslib": "^2.4.0", - "typescript": "^4.8.4", - "vite": "4.2.3" - }, - "config": { - "commitizen": { - "path": "cz-conventional-changelog" - } + "@babel/core": "7.23.3", + "@babel/preset-typescript": "7.23.3", + "@types/jest": "29.5.8", + "@types/node": "20.9.0", + "@vitejs/plugin-vue": "4.4.1", + "@vue/test-utils": "2.4.1", + "@vue/vue3-jest": "29.2.6", + "babel-jest": "29.7.0", + "jest": "29.7.0", + "jest-environment-jsdom": "29.7.0", + "jsdom": "22.1.0", + "prettier": "3.0.3", + "sass": "1.69.5", + "ts-jest": "29.1.1", + "ts-node": "10.9.1", + "tslib": "2.6.2", + "typescript": "4.9.5", + "vite": "4.5.0" } } diff --git a/ui/yarn.lock b/ui/yarn.lock index 4a0ccb114..b42ad402c 100644 --- a/ui/yarn.lock +++ b/ui/yarn.lock @@ -18,38 +18,38 @@ "@babel/highlight" "^7.22.13" chalk "^2.4.2" -"@babel/compat-data@^7.22.20", "@babel/compat-data@^7.22.6", "@babel/compat-data@^7.22.9": - version "7.22.20" - resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.22.20.tgz#8df6e96661209623f1975d66c35ffca66f3306d0" - integrity sha512-BQYjKbpXjoXwFW5jGqiizJQQT/aC7pFm9Ok1OWssonuguICi264lbgMzRp2ZMmRSlfkX6DsWDDcsrctK8Rwfiw== +"@babel/compat-data@^7.22.9": + version "7.23.3" + resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.23.3.tgz#3febd552541e62b5e883a25eb3effd7c7379db11" + integrity sha512-BmR4bWbDIoFJmJ9z2cZ8Gmm2MXgEDgjdWgpKmKWUt54UGFJdlj31ECtbaDvCG/qVdG3AQ1SfpZEs01lUFbzLOQ== -"@babel/core@^7.11.6", "@babel/core@^7.12.3": - version "7.23.0" - resolved 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-cachedir@2.3.0: - version "2.3.0" - resolved "https://registry.yarnpkg.com/cachedir/-/cachedir-2.3.0.tgz#0c75892a052198f0b21c7c1804d8331edfcae0e8" - integrity sha512-A+Fezp4zxnit6FanDmv9EqXNAi3vt9DWp51/71UEhXukb7QUuvtv9344h91dyAxuTLoSYJFU299qzR3tzwPAhw== - callsites@^3.0.0: version "3.1.0" resolved "https://registry.yarnpkg.com/callsites/-/callsites-3.1.0.tgz#b3630abd8943432f54b3f0519238e33cd7df2f73" @@ -2028,12 +1270,12 @@ camelcase@^6.2.0: resolved "https://registry.yarnpkg.com/camelcase/-/camelcase-6.3.0.tgz#5685b95eb209ac9c0c177467778c9c84df58ba9a" integrity sha512-Gmy6FhYlCY7uOElZUSbxo2UCDH8owEk996gkbrpsgGtrJLM3J7jGxl9Ic7Qwwj4ivOE5AWZWRMecDdF7hqGjFA== -caniuse-lite@^1.0.30001517, caniuse-lite@^1.0.30001538: - version "1.0.30001539" - resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001539.tgz#325a387ab1ed236df2c12dc6cd43a4fff9903a44" - integrity sha512-hfS5tE8bnNiNvEOEkm8HElUHroYwlqMMENEzELymy77+tJ6m+gA2krtHl5hxJaj71OlpC2cHZbdSMX1/YEqEkA== +caniuse-lite@^1.0.30001541: + version "1.0.30001561" + resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001561.tgz#752f21f56f96f1b1a52e97aae98c57c562d5d9da" + integrity sha512-NTt0DNoKe958Q0BE0j0c1V9jbUzhBxHIEJy7asmGrpE0yG63KTV7PLHPnK2E1O9RsQrQ081I3NLuXGS6zht3cw== -chalk@^2.1.0, chalk@^2.4.1, chalk@^2.4.2: +chalk@^2.1.0, chalk@^2.4.2: version "2.4.2" resolved "https://registry.yarnpkg.com/chalk/-/chalk-2.4.2.tgz#cd42541677a54333cf541a49108c1432b44c9424" integrity sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ== @@ -2042,7 +1284,7 @@ chalk@^2.1.0, chalk@^2.4.1, chalk@^2.4.2: escape-string-regexp "^1.0.5" supports-color "^5.3.0" -chalk@^4.0.0, chalk@^4.1.0, chalk@^4.1.1: +chalk@^4.0.0: version "4.1.2" resolved "https://registry.yarnpkg.com/chalk/-/chalk-4.1.2.tgz#aac4e2b7734a740867aeb16bf02aad556a1e7a01" integrity sha512-oKnbhFyRIXpUuez8iBMmyEa4nbj4IOQyuhc/wy9kY7/WVPcwIO9VA668Pu8RkO7+0G76SLROeyw9CpQ061i4mA== @@ -2055,11 +1297,6 @@ char-regex@^1.0.2: resolved "https://registry.yarnpkg.com/char-regex/-/char-regex-1.0.2.tgz#d744358226217f981ed58f479b1d6bcc29545dcf" integrity sha512-kWWXztvZ5SBQV+eRgKFeh8q5sLuZY2+8WUIzlxWVTg+oGwY14qylx1KbKzHd8P6ZYkAg0xyIDU9JMHhyJMZ1jw== -chardet@^0.7.0: - version "0.7.0" - resolved "https://registry.yarnpkg.com/chardet/-/chardet-0.7.0.tgz#90094849f0937f2eedc2425d0d28a9e5f0cbad9e" - integrity sha512-mT8iDcrh03qDGRRmoA2hmBJnxpllMR+0/0qlzjqZES6NdiWDcZkCNAk4rPFZ9Q85r27unkiNNg8ZOiwZXBHwcA== - "chokidar@>=3.0.0 <4.0.0": version "3.5.3" resolved "https://registry.yarnpkg.com/chokidar/-/chokidar-3.5.3.tgz#1cf37c8707b932bd1af1ae22c0432e2acd1903bd" @@ -2076,32 +1313,15 @@ chardet@^0.7.0: fsevents "~2.3.2" ci-info@^3.2.0: - version "3.8.0" - resolved "https://registry.yarnpkg.com/ci-info/-/ci-info-3.8.0.tgz#81408265a5380c929f0bc665d62256628ce9ef91" - integrity sha512-eXTggHWSooYhq49F2opQhuHWgzucfF2YgODK4e1566GQs5BIfP30B0oenwBJHfWxAs2fyPB1s7Mg949zLf61Yw== + version "3.9.0" + 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"^1.3.4" proto-list "~1.2.1" -conventional-commit-types@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/conventional-commit-types/-/conventional-commit-types-3.0.0.tgz#7c9214e58eae93e85dd66dbfbafe7e4fffa2365b" - integrity sha512-SmmCYnOniSsAa9GqWOeLqc179lfr5TRu5b4QFDkbsrJ5TZjPJx85wtOr3zn+1dbeNiXDKGPbZ72IKbPhLXh/Lg== - convert-source-map@^1.6.0: version "1.9.0" resolved "https://registry.yarnpkg.com/convert-source-map/-/convert-source-map-1.9.0.tgz#7faae62353fb4213366d0ca98358d22e8368b05f" @@ -2210,28 +1400,6 @@ convert-source-map@^2.0.0: resolved "https://registry.yarnpkg.com/convert-source-map/-/convert-source-map-2.0.0.tgz#4b560f649fc4e918dd0ab75cf4961e8bc882d82a" integrity sha512-Kvp459HrV2FEJ1CAsi1Ku+MY3kasH19TFykTz2xWmMeq6bk2NU3XXvfJ+Q61m0xktWwt+1HSYf3JZsTms3aRJg== -core-js-compat@^3.31.0: - version "3.32.2" - resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.32.2.tgz#8047d1a8b3ac4e639f0d4f66d4431aa3b16e004c" - integrity 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+1452,17 @@ cssstyle@^2.3.0: dependencies: cssom "~0.3.6" -csstype@^2.6.8: - version "2.6.21" - resolved "https://registry.yarnpkg.com/csstype/-/csstype-2.6.21.tgz#2efb85b7cc55c80017c66a5ad7cbd931fda3a90e" - integrity sha512-Z1PhmomIfypOpoMjRQB70jfvy/wxT50qW08YXO5lMIJkrdq4yOTR+AW7FqutScmB9NkLwxo+jU+kZLbofZZq/w== - -cz-conventional-changelog@3.3.0: - version "3.3.0" - resolved "https://registry.yarnpkg.com/cz-conventional-changelog/-/cz-conventional-changelog-3.3.0.tgz#9246947c90404149b3fe2cf7ee91acad3b7d22d2" - integrity sha512-U466fIzU5U22eES5lTNiNbZ+d8dfcHcssH4o7QsdWaCcRs/feIPCxKYSWkYBNs5mny7MvEfwpTLWjvbm94hecw== - dependencies: - chalk "^2.4.1" - commitizen "^4.0.3" - conventional-commit-types "^3.0.0" - lodash.map "^4.5.1" - longest "^2.0.1" - word-wrap "^1.0.3" - optionalDependencies: - "@commitlint/load" ">6.1.1" +cssstyle@^3.0.0: + version "3.0.0" + resolved "https://registry.yarnpkg.com/cssstyle/-/cssstyle-3.0.0.tgz#17ca9c87d26eac764bb8cfd00583cff21ce0277a" + integrity 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"https://registry.yarnpkg.com/debug/-/debug-4.3.4.tgz#1319f6579357f2338d3337d2cdd4914bb5dcc865" @@ -2319,16 +1489,11 @@ debug@4, debug@^4.1.0, debug@^4.1.1: dependencies: ms "2.1.2" -decimal.js@^10.4.2: +decimal.js@^10.4.2, decimal.js@^10.4.3: version "10.4.3" resolved "https://registry.yarnpkg.com/decimal.js/-/decimal.js-10.4.3.tgz#1044092884d245d1b7f65725fa4ad4c6f781cc23" integrity sha512-VBBaLc1MgL5XpzgIP7ny5Z6Nx3UrRkIViUkPUdtl9aya5amy3De1gsUUSB1g3+3sExYNjCAsAznmukyxCb1GRA== -dedent@0.7.0: - version "0.7.0" - resolved "https://registry.yarnpkg.com/dedent/-/dedent-0.7.0.tgz#2495ddbaf6eb874abb0e1be9df22d2e5a544326c" - integrity sha512-Q6fKUPqnAHAyhiUgFU7BUzLiv0kd8saH9al7tnu5Q/okj6dnupxyTgFIBjVzJATdfIAm9NAsvXNzjaKa+bxVyA== - dedent@^1.0.0: version "1.5.1" resolved "https://registry.yarnpkg.com/dedent/-/dedent-1.5.1.tgz#4f3fc94c8b711e9bb2800d185cd6ad20f2a90aff" @@ -2339,28 +1504,11 @@ deepmerge@^4.2.2: resolved 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sha512-DtCOLG98P007x7wiiOmfI0fi3eIKyWiLTGJ2MDnVi/E04lWGbf+JzrRHMm0rgIIZJGtHpKpbVgLWHrv8xXpc3Q== - -detect-indent@6.1.0: - version "6.1.0" - resolved "https://registry.yarnpkg.com/detect-indent/-/detect-indent-6.1.0.tgz#592485ebbbf6b3b1ab2be175c8393d04ca0d57e6" - integrity sha512-reYkTUJAZb9gUuZ2RvVCNhVHdg62RHnJ7WJl8ftMi4diZ6NWlciOzQN88pUhSELEwflJht4oQDv0F0BMlwaYtA== - detect-newline@^3.0.0: version "3.1.0" resolved "https://registry.yarnpkg.com/detect-newline/-/detect-newline-3.1.0.tgz#576f5dfc63ae1a192ff192d8ad3af6308991b651" @@ -2393,10 +1541,10 @@ editorconfig@^1.0.3: minimatch "9.0.1" semver "^7.5.3" -electron-to-chromium@^1.4.477, electron-to-chromium@^1.4.526: - version "1.4.529" - resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.529.tgz#8c3377a05e5737f899770d14524dd8e2e4cb2351" - integrity sha512-6uyPyXTo8lkv8SWAmjKFbG42U073TXlzD4R8rW3EzuznhFS2olCIAfjjQtV2dV2ar/vRF55KUd3zQYnCB0dd3A== +electron-to-chromium@^1.4.535: + version "1.4.580" + resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.580.tgz#2f8f70f70733a6be1fb6f31de1224e6dc4bb196d" + integrity sha512-T5q3pjQon853xxxHUq3ZP68ZpvJHuSMY2+BZaW3QzjS4HvNuvsMmZ/+lU+nCrftre1jFZ+OSlExynXWBihnXzw== emittery@^0.13.1: version "0.13.1" @@ -2420,33 +1568,33 @@ error-ex@^1.3.1: dependencies: is-arrayish "^0.2.1" -esbuild@^0.17.5: - version "0.17.19" - resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.17.19.tgz#087a727e98299f0462a3d0bcdd9cd7ff100bd955" - integrity sha512-XQ0jAPFkK/u3LcVRcvVHQcTIqD6E2H1fvZMA5dQPSOWb3suUbWbfbRf94pjc0bNzRYLfIrDRQXr7X+LHIm5oHw== +esbuild@^0.18.10: + version "0.18.20" + resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.18.20.tgz#4709f5a34801b43b799ab7d6d82f7284a9b7a7a6" + integrity sha512-ceqxoedUrcayh7Y7ZX6NdbbDzGROiyVBgC4PriJThBKSVPWnnFHZAkfI1lJT8QFkOwH4qOS2SJkS4wvpGl8BpA== optionalDependencies: - "@esbuild/android-arm" "0.17.19" - "@esbuild/android-arm64" "0.17.19" - "@esbuild/android-x64" 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"https://registry.yarnpkg.com/find-node-modules/-/find-node-modules-2.1.3.tgz#3c976cff2ca29ee94b4f9eafc613987fc4c0ee44" - integrity sha512-UC2I2+nx1ZuOBclWVNdcnbDR5dlrOdVb7xNjmT/lHE+LsgztWks3dG7boJ37yTS/venXw84B/mAW9uHVoC5QRg== - dependencies: - findup-sync "^4.0.0" - merge "^2.1.1" - -find-root@1.1.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/find-root/-/find-root-1.1.0.tgz#abcfc8ba76f708c42a97b3d685b7e9450bfb9ce4" - integrity sha512-NKfW6bec6GfKc0SGx1e07QZY9PE99u0Bft/0rzSD5k3sO/vwkVUpDUKVm5Gpp5Ue3YfShPFTX2070tDs5kB9Ng== - find-up@^4.0.0, find-up@^4.1.0: version "4.1.0" resolved "https://registry.yarnpkg.com/find-up/-/find-up-4.1.0.tgz#97afe7d6cdc0bc5928584b7c8d7b16e8a9aa5d19" @@ -2593,16 +1700,6 @@ find-up@^4.0.0, find-up@^4.1.0: locate-path "^5.0.0" path-exists "^4.0.0" -findup-sync@^4.0.0: - version "4.0.0" - resolved "https://registry.yarnpkg.com/findup-sync/-/findup-sync-4.0.0.tgz#956c9cdde804052b881b428512905c4a5f2cdef0" - integrity 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"https://registry.yarnpkg.com/function-bind/-/function-bind-1.1.2.tgz#2c02d864d97f3ea6c8830c464cbd11ab6eab7a1c" + integrity sha512-7XHNxH7qX9xG5mIwxkhumTox/MIRNcOgDrxWsMt2pAr23WHp6MrRlN7FBSFpCpr+oVO0F744iUgR82nJMfG2SA== gensync@^1.0.0-beta.2: version "1.0.0-beta.2" @@ -2669,7 +1751,7 @@ glob-parent@~5.1.2: dependencies: is-glob "^4.0.1" -glob@7.2.3, glob@^7.1.3, glob@^7.1.4: +glob@^7.1.3, glob@^7.1.4: version "7.2.3" resolved "https://registry.yarnpkg.com/glob/-/glob-7.2.3.tgz#b8df0fb802bbfa8e89bd1d938b4e16578ed44f2b" integrity sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q== @@ -2692,39 +1774,12 @@ glob@^8.1.0: minimatch "^5.0.1" once "^1.3.0" -global-dirs@^0.1.1: - version "0.1.1" - resolved "https://registry.yarnpkg.com/global-dirs/-/global-dirs-0.1.1.tgz#b319c0dd4607f353f3be9cca4c72fc148c49f445" - integrity sha512-NknMLn7F2J7aflwFOlGdNIuCDpN3VGoSoB+aap3KABFWbHVn1TCgFC+np23J8W2BiZbjfEw3BFBycSMv1AFblg== - dependencies: - ini "^1.3.4" - -global-modules@^1.0.0: - version "1.0.0" - resolved "https://registry.yarnpkg.com/global-modules/-/global-modules-1.0.0.tgz#6d770f0eb523ac78164d72b5e71a8877265cc3ea" - integrity sha512-sKzpEkf11GpOFuw0Zzjzmt4B4UZwjOcG757PPvrfhxcLFbq0wpsgpOqxpxtxFiCG4DtG93M6XRVbF2oGdev7bg== - dependencies: - global-prefix "^1.0.1" - is-windows "^1.0.1" - resolve-dir "^1.0.0" - -global-prefix@^1.0.1: - version "1.0.2" - resolved "https://registry.yarnpkg.com/global-prefix/-/global-prefix-1.0.2.tgz#dbf743c6c14992593c655568cb66ed32c0122ebe" - integrity sha512-5lsx1NUDHtSjfg0eHlmYvZKv8/nVqX4ckFbM+FrGcQ+04KWcWFo9P5MxPZYSzUvyzmdTbI7Eix8Q4IbELDqzKg== - dependencies: - expand-tilde "^2.0.2" - homedir-polyfill "^1.0.1" - ini "^1.3.4" - is-windows "^1.0.1" - which "^1.2.14" - globals@^11.1.0: version "11.12.0" resolved "https://registry.yarnpkg.com/globals/-/globals-11.12.0.tgz#ab8795338868a0babd8525758018c2a7eb95c42e" integrity 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< 3" - -ieee754@^1.1.13: - version "1.2.1" - resolved "https://registry.yarnpkg.com/ieee754/-/ieee754-1.2.1.tgz#8eb7a10a63fff25d15a57b001586d177d1b0d352" - integrity sha512-dcyqhDvX1C46lXZcVqCpK+FtMRQVdIMN6/Df5js2zouUsqG7I6sFxitIC+7KYK29KdXOLHdu9zL4sFnoVQnqaA== - immutable@^4.0.0: - version "4.3.1" - resolved "https://registry.yarnpkg.com/immutable/-/immutable-4.3.1.tgz#17988b356097ab0719e2f741d56f3ec6c317f9dc" - integrity sha512-lj9cnmB/kVS0QHsJnYKD1uo3o39nrbKxszjnqS9Fr6NB7bZzW45U6WSGBPKXDL/CvDKqDNPA4r3DoDQ8GTxo2A== - -import-fresh@^3.0.0, import-fresh@^3.2.1: - version "3.3.0" - resolved "https://registry.yarnpkg.com/import-fresh/-/import-fresh-3.3.0.tgz#37162c25fcb9ebaa2e6e53d5b4d88ce17d9e0c2b" - integrity sha512-veYYhQa+D1QBKznvhUHxb8faxlrwUnxseDAbAp457E0wLNio2bOSKnjYDhMj+YiAq61xrMGhQk9iXVk5FzgQMw== - dependencies: - parent-module "^1.0.0" - resolve-from "^4.0.0" + version "4.3.4" + resolved "https://registry.yarnpkg.com/immutable/-/immutable-4.3.4.tgz#2e07b33837b4bb7662f288c244d1ced1ef65a78f" + integrity sha512-fsXeu4J4i6WNWSikpI88v/PcVflZz+6kMhUfIwc5SY+poQRPnaf5V7qds6SUyUN3cVxEzuCab7QIoLOQ+DQ1wA== import-local@^3.0.2: version "3.1.0" @@ -2840,7 +1868,7 @@ inflight@^1.0.4: once "^1.3.0" wrappy "1" -inherits@2, inherits@^2.0.3, inherits@^2.0.4: +inherits@2: version "2.0.4" resolved "https://registry.yarnpkg.com/inherits/-/inherits-2.0.4.tgz#0fa2c64f932917c3433a0ded55363aae37416b7c" integrity sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ== @@ -2850,27 +1878,6 @@ ini@^1.3.4: resolved "https://registry.yarnpkg.com/ini/-/ini-1.3.8.tgz#a29da425b48806f34767a4efce397269af28432c" integrity sha512-JV/yugV2uzW5iMRSiZAyDtQd+nxtUnjeLt0acNdw98kKLrvuRVyB80tsREOE7yvGVgalhZ6RNXCmEHkUKBKxew== -inquirer@8.2.5: - version "8.2.5" - resolved "https://registry.yarnpkg.com/inquirer/-/inquirer-8.2.5.tgz#d8654a7542c35a9b9e069d27e2df4858784d54f8" - 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- ci-info "^3.2.0" - graceful-fs "^4.2.9" - picomatch "^2.2.3" - -jest-util@^29.7.0: +jest-util@^29.0.0, jest-util@^29.7.0: version "29.7.0" resolved "https://registry.yarnpkg.com/jest-util/-/jest-util-29.7.0.tgz#23c2b62bfb22be82b44de98055802ff3710fc0bc" integrity sha512-z6EbKajIpqGKU56y5KBUgy1dt1ihhQJgWzUlZHArA/+X2ad7Cb5iF+AK1EWVL/Bo7Rz9uurpqw6SiBCefUbCGA== @@ -3379,7 +2354,7 @@ jest-worker@^29.7.0: merge-stream "^2.0.0" supports-color "^8.0.0" -jest@^29.0.3: +jest@29.7.0: version "29.7.0" resolved "https://registry.yarnpkg.com/jest/-/jest-29.7.0.tgz#994676fc24177f088f1c5e3737f5697204ff2613" integrity sha512-NIy3oAFp9shda19hy4HK0HRTWKtPJmGdnvywu01nOqNC2vZg+Z+fvJDxpMQA88eb2I9EcafcdjYgsDthnYTvGw== @@ -3412,14 +2387,36 @@ js-yaml@^3.13.1: argparse "^1.0.7" esprima "^4.0.0" -js-yaml@^4.1.0: - version "4.1.0" - resolved "https://registry.yarnpkg.com/js-yaml/-/js-yaml-4.1.0.tgz#c1fb65f8f5017901cdd2c951864ba18458a10602" - integrity 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"@vue/devtools-api" "^6.5.0" -vue@3.2.47: - version "3.2.47" - resolved "https://registry.yarnpkg.com/vue/-/vue-3.2.47.tgz#3eb736cbc606fc87038dbba6a154707c8a34cff0" - integrity sha512-60188y/9Dc9WVrAZeUVSDxRQOZ+z+y5nO2ts9jWXSTkMvayiWxCWOWtBQoYjLeccfXkiiPZWAHcV+WTPhkqJHQ== +vue@3.3.8: + version "3.3.8" + resolved "https://registry.yarnpkg.com/vue/-/vue-3.3.8.tgz#532ff071af24f6a69e5ecc53a66858a9ee874ffc" + integrity sha512-5VSX/3DabBikOXMsxzlW8JyfeLKlG9mzqnWgLQLty88vdZL7ZJgrdgBOmrArwxiLtmS+lNNpPcBYqrhE6TQW5w== dependencies: - "@vue/compiler-dom" "3.2.47" - "@vue/compiler-sfc" "3.2.47" - "@vue/runtime-dom" "3.2.47" - "@vue/server-renderer" "3.2.47" - "@vue/shared" "3.2.47" + "@vue/compiler-dom" "3.3.8" + "@vue/compiler-sfc" "3.3.8" + "@vue/runtime-dom" "3.3.8" + "@vue/server-renderer" "3.3.8" + "@vue/shared" "3.3.8" w3c-xmlserializer@^4.0.0: version "4.0.0" @@ -4512,13 +3226,6 @@ walker@^1.0.8: dependencies: makeerror "1.0.12" -wcwidth@^1.0.1: - version "1.0.1" - resolved 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sha512-Ed/LrqB8EPlGxjS+TrsXcpUond1mhccS3pchLhzSgPCnTimUCKj3IZE75pAs5m6heB2U2TMerKFUXheyHY+VDQ== dependencies: - isexe "^2.0.0" + tr46 "^4.1.1" + webidl-conversions "^7.0.0" which@^2.0.1: version "2.0.2" @@ -4558,11 +3266,6 @@ which@^2.0.1: dependencies: isexe "^2.0.0" -word-wrap@^1.0.3: - version "1.2.5" - resolved "https://registry.yarnpkg.com/word-wrap/-/word-wrap-1.2.5.tgz#d2c45c6dd4fbce621a66f136cbe328afd0410b34" - integrity sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA== - wrap-ansi@^7.0.0: version "7.0.0" resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" @@ -4585,7 +3288,7 @@ write-file-atomic@^4.0.2: imurmurhash "^0.1.4" signal-exit "^3.0.7" -ws@^8.11.0: +ws@^8.11.0, ws@^8.13.0: version "8.14.2" resolved "https://registry.yarnpkg.com/ws/-/ws-8.14.2.tgz#6c249a806eb2db7a20d26d51e7709eab7b2e6c7f" integrity 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