From ec5309fa169401992d8d48be762c04f55ef1d864 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Wed, 4 Oct 2023 17:33:41 +0000 Subject: [PATCH] Built site for sdtm.oak: 0.0.0.9000@3657637 --- main/404.html | 6 --- main/CODE_OF_CONDUCT.html | 6 --- main/CONTRIBUTING.html | 84 ++++++++++++++++++++++++++++++--- main/LICENSE.html | 6 --- main/authors.html | 6 --- main/index.html | 6 --- main/news/index.html | 6 --- main/pkgdown.yml | 2 +- main/pull_request_template.html | 6 --- main/reference/index.html | 6 --- main/reference/sdtm.oak.html | 6 --- main/search.json | 2 +- 12 files changed, 80 insertions(+), 62 deletions(-) diff --git a/main/404.html b/main/404.html index f31d3b47..9313e91d 100644 --- a/main/404.html +++ b/main/404.html @@ -39,12 +39,6 @@
  • Changelog
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    main
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    Type 2 Contribution without Code:The {oak} core development team will contact the issue creator as soon as possible to discuss further details.

    See Contribution to {admiral} for additional details.

    + +
    +

    Containers guideline

    +

    This guideline will walk you through the process of setting up and using the Oak image in both GitHub Codespaces and Visual Studio Code’s devcontainer functionality.

    +
    +

    Use GitHub Codespaces

    +
    1. +Prerequisites :
      2. +
    • Have a GitHub account.
      • +
    • The repository you want to open in Codespaces must be under your account or you must have appropriate permissions.
      • +
    1. +Open the Repository :
      2. +
    • Navigate to the desired GitHub repository on GitHub’s website.
      • +
    1. +Start Codespaces :
      2. +
    • Click on the “Code” button (it has a green color most of the times).
      • +
    • In the dropdown, you’ll find an option named “Open with Codespaces”. Click on it.
      • +
    1. +Choose or Create a Codespace :
      2. +
    • If you’ve already created a Codespace for this repository, you’ll see it listed. You can click on it to open.
      • +
    • If not, click on the “+ New codespace” button.
      • +
    1. +Configure the Environment (If needed) :
      2. +
    • Depending on the repository, you might have a .devcontainer folder which will define the environment. GitHub Codespaces will use the settings defined here to set up the environment.
      • +
    • If you need to customize or install additional tools, you can do so once the Codespace is launched.
      • +
    1. +Use Codespaces :
      2. +
    • Once your environment is set up, you’ll have an instance of Visual Studio Code running in your browser, connected to the repository.
      • +
    • You can now edit, run, and debug your code just like you would in a local environment.
      • +
    1. +Close the Codespace :
      2. +
    • When you’re done, you can close the browser tab/window.
      • +
    • Remember, you’ll be billed (if you’re on a paid plan) for the time your Codespace is running, so it’s a good idea to stop or delete it if you’re not using it. You can do this from the Codespaces tab in your GitHub repository.
      • +
    +
    +

    Use Visual Code devcontainer

    +
    1. +Prerequisites :
      2. +
    • Have a Docker and VS Code installed
      • +
    • linux/arm64 is supported only for R 4.3
      • +
    1. +Install devcontainer extension :
      2. +
    • In the left sidebar, click on the extensions icon (it looks like square blocks or a Lego piece).
      • +
    • In the search bar, type “Dev Containers” to search for the extension.
      • +
    • From the search results, locate the “Dev Containers” extension provided by Microsoft and click the ‘Install’ button.
      • +
    1. +Open in Container :
      2. +
    • In VS Code, use the command palette (Ctrl+Shift+P or Cmd+Shift+P on macOS) and run the “Dev Containers: Rebuild and Reopen in Container” command. VS Code will then set up the devcontainer using the Oak image.
      • +
    1. +Using the Devcontainer :
      2. +
    • Once the environment is set up, you can start coding in VS Code as if you were in a local environment, but with the capabilities and tools provided by the Oak image.
      • +
    +
    +

    Use docker run

    +
    1. +Prerequisites :
      2. +
    • Have a docker installed
      • +
    1. +Example command :
      2. +
    docker run --rm -d \
+  --name oak-dev \
+  -p 127.0.0.1:8888:8787 \
+  -e ROOT=true -e DISABLE_AUTH=true \
+  -v "$(pwd):/home/rstudio/oak" \
+  ghcr.io/pharmaverse/sdtm.oak-4.3:latest
    +

    This command is used to start a new container from a Docker image. Here’s a breakdown of the parameters used:

    +
    • docker run: This is the basic command to start a new container from a Docker image.
      • +
    • –rm: This option ensures that the container is removed automatically when it’s stopped. This is useful if you don’t want to keep the container around once you’re done with it, helping to save storage space.
      • +
    • -d: This option runs the container in detached mode, which means the container runs in the background and doesn’t attach to your command line session.
      • +
    • –name oak-dev: This assigns the name oak-dev to the container. Naming your containers makes them easier to identify and manage.
      • +
    • -p 127.0.0.1:8888:8787: This maps port 8787 inside the container to port 8888 on the host machine, and binds it to the localhost IP (127.0.0.1). The format is -p ::. This means any traffic directed at port 8888 on your host machine will be forwarded to port 8787 in the container.
      • +
    • -e ROOT=true -e DISABLE_AUTH=true: These are environment variables being passed into the container. -e denotes that an environment variable is being set. In this case, two environment variables are being set: +
      • ROOT=true: This likely grants root permissions inside the container.
        • +
      • DISABLE_AUTH=true: This likely disables authentication when opening RStudio.
        • +
      • +
    • -v “$(pwd):/home/rstudio/oak”: This maps a volume (essentially a directory) from the host machine into the container. The $(pwd) is a command that returns the current directory you’re in on the host machine. This current directory is then mapped to /home/rstudio/oak inside the container. This is useful for sharing files between your host machine and the container.
      • +
    • ghcr.io/pharmaverse/sdtm.oak-4.3:latest: This is the name of the Docker image that the container will be created from. It’s pulled from the GitHub Container Registry (ghcr.io) and the image belongs to the pharmaverse repository. The image name is sdtm.oak-4.3 and the tag being used is latest. There are image for three versions available.
      • +
    diff --git a/main/LICENSE.html b/main/LICENSE.html index 953bb800..181fc6cf 100644 --- a/main/LICENSE.html +++ b/main/LICENSE.html @@ -24,12 +24,6 @@
  • Changelog
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  • Changelog
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    main
    • - diff --git a/main/reference/sdtm.oak.html b/main/reference/sdtm.oak.html index ba0dd9a7..43c65a2f 100644 --- a/main/reference/sdtm.oak.html +++ b/main/reference/sdtm.oak.html @@ -32,12 +32,6 @@
  • Changelog
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    • - diff --git a/main/search.json b/main/search.json index c8a86ff0..4b1af879 100644 --- a/main/search.json +++ b/main/search.json @@ -1 +1 @@ -[{"path":"/CODE_OF_CONDUCT.html","id":null,"dir":"","previous_headings":"","what":"Contributor Code of Conduct","title":"Contributor Code of Conduct","text":"contributors maintainers project, pledge respect people contribute reporting issues, posting feature requests, updating documentation, submitting pull requests patches, activities. committed making participation project harassment-free experience everyone, regardless level experience, gender, gender identity expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion. Examples unacceptable behavior participants include use sexual language imagery, derogatory comments personal attacks, trolling, public private harassment, insults, unprofessional conduct. Project maintainers right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct. Project maintainers follow Code Conduct may removed project team. Instances abusive, harassing, otherwise unacceptable behavior may reported opening issue contacting one project maintainers. 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Copyright holder, funder.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Garcia O, Ganapathy R (2023). sdtm.oak: SDTM Data Transformation Engine. https://pharmaverse.github.io/oak/, https://github.com/pharmaverse/oak.","code":"@Manual{, title = {sdtm.oak: SDTM Data Transformation Engine}, author = {Omar Garcia and Rammprasad Ganapathy}, year = {2023}, note = {https://pharmaverse.github.io/oak/, https://github.com/pharmaverse/oak}, }"},{"path":"/index.html","id":"sdtmoak","dir":"","previous_headings":"","what":"SDTM Data Transformation Engine","title":"SDTM Data Transformation Engine","text":"EDC Data Standard agnostic SDTM data transformation engine automates transformation raw clinical data ODM format SDTM based standard mapping algorithms","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"SDTM Data Transformation Engine","text":"can install development version sdtm.oak GitHub :","code":"# install.packages(\"remotes\") remotes::install_github(\"pharmaverse/oak\")"},{"path":"/reference/sdtm.oak.html","id":null,"dir":"Reference","previous_headings":"","what":"An EDC and Data Standard agnostic SDTM data transformation engine that automates\nthe transformation of raw clinical data in ODM format to SDTM based on standard\nmapping algorithms — sdtm.oak","title":"An EDC and Data Standard agnostic SDTM data transformation engine that automates\nthe transformation of raw clinical data in ODM format to SDTM based on standard\nmapping algorithms — sdtm.oak","text":"EDC Data Standard agnostic SDTM data transformation engine automates transformation raw clinical data ODM format SDTM based standard mapping algorithms","code":""},{"path":"/news/index.html","id":"sdtmoak-development-version","dir":"Changelog","previous_headings":"","what":"sdtm.oak (development version)","title":"sdtm.oak (development version)","text":"Initial CRAN submission.","code":""}] +[{"path":"/CODE_OF_CONDUCT.html","id":null,"dir":"","previous_headings":"","what":"Contributor Code of Conduct","title":"Contributor Code of Conduct","text":"contributors maintainers project, pledge respect people contribute reporting issues, posting feature requests, updating documentation, submitting pull requests patches, activities. committed making participation project harassment-free experience everyone, regardless level experience, gender, gender identity expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, religion. Examples unacceptable behavior participants include use sexual language imagery, derogatory comments personal attacks, trolling, public private harassment, insults, unprofessional conduct. Project maintainers right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct. Project maintainers follow Code Conduct may removed project team. Instances abusive, harassing, otherwise unacceptable behavior may reported opening issue contacting one project maintainers. 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Since 100% fully resourced software development team might issues take longer respond depending amount overall issues. Familiarize programming strategy, guidance GitHub usage unit testing. newly created issues reviewed within next backlog meeting creator receive initial feedback via comment. Someone core development team triage new issues assigning appropriate labels (“user request” can easily identify new requests). Issues meant taken users Pharma programming community.","code":""},{"path":[]},{"path":"/CONTRIBUTING.html","id":"type-1-contribution-with-code","dir":"","previous_headings":"","what":"Type 1 Contribution with Code:","title":"Contribution to {oak}","text":"First, user creates issue comments existing issue notify ’d like contribute code. Follow development process step--step guide. advise contact {oak} core development team directly via Slack submitting code complex functionality.","code":""},{"path":"/CONTRIBUTING.html","id":"type-2-contribution-without-code","dir":"","previous_headings":"","what":"Type 2 Contribution without Code:","title":"Contribution to {oak}","text":"User creates issue ideally contacts {oak} team member via Slack. {oak} core development team contact issue creator soon possible discuss details. See Contribution {admiral} additional details.","code":""},{"path":"/CONTRIBUTING.html","id":"containers-guideline","dir":"","previous_headings":"","what":"Containers guideline","title":"Contribution to {oak}","text":"guideline walk process setting using Oak image GitHub Codespaces Visual Studio Code’s devcontainer functionality.","code":""},{"path":"/CONTRIBUTING.html","id":"use-github-codespaces","dir":"","previous_headings":"","what":"Use GitHub Codespaces","title":"Contribution to {oak}","text":"Prerequisites : GitHub account. repository want open Codespaces must account must appropriate permissions. Open Repository : Navigate desired GitHub repository GitHub’s website. Start Codespaces : Click “Code” button (green color times). dropdown, ’ll find option named “Open Codespaces”. Click . Choose Create Codespace : ’ve already created Codespace repository, ’ll see listed. can click open. , click “+ New codespace” button. Configure Environment (needed) : Depending repository, might .devcontainer folder define environment. GitHub Codespaces use settings defined set environment. need customize install additional tools, can Codespace launched. Use Codespaces : environment set , ’ll instance Visual Studio Code running browser, connected repository. can now edit, run, debug code just like local environment. Close Codespace : ’re done, can close browser tab/window. Remember, ’ll billed (’re paid plan) time Codespace running, ’s good idea stop delete ’re using . can Codespaces tab GitHub repository.","code":""},{"path":"/CONTRIBUTING.html","id":"use-visual-code-devcontainer","dir":"","previous_headings":"","what":"Use Visual Code devcontainer","title":"Contribution to {oak}","text":"Prerequisites : Docker VS Code installed linux/arm64 supported R 4.3 Install devcontainer extension : left sidebar, click extensions icon (looks like square blocks Lego piece). search bar, type “Dev Containers” search extension. search results, locate “Dev Containers” extension provided Microsoft click ‘Install’ button. Open Container : VS Code, use command palette (Ctrl+Shift+P Cmd+Shift+P macOS) run “Dev Containers: Rebuild Reopen Container” command. VS Code set devcontainer using Oak image. Using Devcontainer : environment set , can start coding VS Code local environment, capabilities tools provided Oak image.","code":""},{"path":"/CONTRIBUTING.html","id":"use-docker-run","dir":"","previous_headings":"","what":"Use docker run","title":"Contribution to {oak}","text":"Prerequisites : docker installed Example command : command used start new container Docker image. ’s breakdown parameters used: docker run: basic command start new container Docker image. –rm: option ensures container removed automatically ’s stopped. useful don’t want keep container around ’re done , helping save storage space. -d: option runs container detached mode, means container runs background doesn’t attach command line session. –name oak-dev: assigns name oak-dev container. Naming containers makes easier identify manage. -p 127.0.0.1:8888:8787: maps port 8787 inside container port 8888 host machine, binds localhost IP (127.0.0.1). format -p ::. means traffic directed port 8888 host machine forwarded port 8787 container. ROOT=true: likely grants root permissions inside container. DISABLE_AUTH=true: likely disables authentication opening RStudio. -v “$(pwd):/home/rstudio/oak”: maps volume (essentially directory) host machine container. $(pwd) command returns current directory ’re host machine. current directory mapped /home/rstudio/oak inside container. useful sharing files host machine container. ghcr.io/pharmaverse/sdtm.oak-4.3:latest: name Docker image container created . ’s pulled GitHub Container Registry (ghcr.io) image belongs pharmaverse repository. image name sdtm.oak-4.3 tag used latest. image three versions available.","code":"docker run --rm -d \\ --name oak-dev \\ -p 127.0.0.1:8888:8787 \\ -e ROOT=true -e DISABLE_AUTH=true \\ -v \"$(pwd):/home/rstudio/oak\" \\ ghcr.io/pharmaverse/sdtm.oak-4.3:latest"},{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004 ","code":""},{"path":[]},{"path":"/LICENSE.html","id":"id_1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"/LICENSE.html","id":"id_2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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Disclaimer of Warranty","title":"Apache License","text":"Unless required applicable law agreed writing, Licensor provides Work (Contributor provides Contributions) “” BASIS, WITHOUT WARRANTIES CONDITIONS KIND, either express implied, including, without limitation, warranties conditions TITLE, NON-INFRINGEMENT, MERCHANTABILITY, FITNESS PARTICULAR PURPOSE. solely responsible determining appropriateness using redistributing Work assume risks associated exercise permissions License.","code":""},{"path":"/LICENSE.html","id":"id_8-limitation-of-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"8. Limitation of Liability","title":"Apache License","text":"event legal theory, whether tort (including negligence), contract, otherwise, unless required applicable law (deliberate grossly negligent acts) agreed writing, shall Contributor liable damages, including direct, indirect, special, incidental, consequential damages character arising result License use inability use Work (including limited damages loss goodwill, work stoppage, computer failure malfunction, commercial damages losses), even Contributor advised possibility damages.","code":""},{"path":"/LICENSE.html","id":"id_9-accepting-warranty-or-additional-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"9. Accepting Warranty or Additional Liability","title":"Apache License","text":"redistributing Work Derivative Works thereof, may choose offer, charge fee , acceptance support, warranty, indemnity, liability obligations /rights consistent License. However, accepting obligations, may act behalf sole responsibility, behalf Contributor, agree indemnify, defend, hold Contributor harmless liability incurred , claims asserted , Contributor reason accepting warranty additional liability. END TERMS CONDITIONS","code":""},{"path":"/LICENSE.html","id":"appendix-how-to-apply-the-apache-license-to-your-work","dir":"","previous_headings":"","what":"APPENDIX: How to apply the Apache License to your work","title":"Apache License","text":"apply Apache License work, attach following boilerplate notice, fields enclosed brackets [] replaced identifying information. (Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Omar Garcia. Author, maintainer. Rammprasad Ganapathy. Author. F. Hoffmann-La Roche AG. Copyright holder, funder. Pfizer Inc. Copyright holder, funder.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Garcia O, Ganapathy R (2023). sdtm.oak: SDTM Data Transformation Engine. https://pharmaverse.github.io/oak/, https://github.com/pharmaverse/oak.","code":"@Manual{, title = {sdtm.oak: SDTM Data Transformation Engine}, author = {Omar Garcia and Rammprasad Ganapathy}, year = {2023}, note = {https://pharmaverse.github.io/oak/, https://github.com/pharmaverse/oak}, }"},{"path":"/index.html","id":"sdtmoak","dir":"","previous_headings":"","what":"SDTM Data Transformation Engine","title":"SDTM Data Transformation Engine","text":"EDC Data Standard agnostic SDTM data transformation engine automates transformation raw clinical data ODM format SDTM based standard mapping algorithms","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"SDTM Data Transformation Engine","text":"can install development version sdtm.oak GitHub :","code":"# install.packages(\"remotes\") remotes::install_github(\"pharmaverse/oak\")"},{"path":"/reference/sdtm.oak.html","id":null,"dir":"Reference","previous_headings":"","what":"An EDC and Data Standard agnostic SDTM data transformation engine that automates\nthe transformation of raw clinical data in ODM format to SDTM based on standard\nmapping algorithms — sdtm.oak","title":"An EDC and Data Standard agnostic SDTM data transformation engine that automates\nthe transformation of raw clinical data in ODM format to SDTM based on standard\nmapping algorithms — sdtm.oak","text":"EDC Data Standard agnostic SDTM data transformation engine automates transformation raw clinical data ODM format SDTM based standard mapping algorithms","code":""},{"path":"/news/index.html","id":"sdtmoak-development-version","dir":"Changelog","previous_headings":"","what":"sdtm.oak (development version)","title":"sdtm.oak (development version)","text":"Initial CRAN submission.","code":""}]