Merge pull request #2 from Sage-Bionetworks/use-golem

Merge @thomasyu888's updates to use Golem for Shiny app structure

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies
+when an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [INSERT CONTACT
+METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/
+code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://
+www.contributor-covenant.org/translations.

DESCRIPTION

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+Package: csbcPsonManifest
+Title: CSBC PSON manifest
+Version: 0.0.0.9000
+Authors@R: person('Verena', 'Chung', email = '[email protected]', role = c('cre', 'aut'))
+Description: A Shiny app to add manifests to the Cancer Complexity Knowledge Portal.
+License: What license is it under?
+Imports: 
+    config,
+    golem,
+    shiny,
+    processx,
+    attempt,
+    DT,
+    glue,
+    htmltools,
+    shinydashboard,
+    waiter
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.1
+Suggests: 
+    testthat,
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr

Dockerfile

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+FROM rocker/r-ver:4.0.2
+RUN apt-get update && apt-get install -y  git-core libcurl4-openssl-dev libgit2-dev libicu-dev libssl-dev libxml2-dev make pandoc pandoc-citeproc && rm -rf /var/lib/apt/lists/*
+RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site
+RUN R -e 'install.packages("remotes")'
+RUN R -e 'remotes::install_github("r-lib/remotes", ref = "97bbf81")'
+RUN Rscript -e 'remotes::install_version("glue",upgrade="never", version = "1.4.1")'
+RUN Rscript -e 'remotes::install_version("processx",upgrade="never", version = "3.4.3")'
+RUN Rscript -e 'remotes::install_version("htmltools",upgrade="never", version = "0.5.0")'
+RUN Rscript -e 'remotes::install_version("knitr",upgrade="never", version = "1.29")'
+RUN Rscript -e 'remotes::install_version("attempt",upgrade="never", version = "0.3.1")'
+RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.5.0")'
+RUN Rscript -e 'remotes::install_version("testthat",upgrade="never", version = "2.3.2")'
+RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.1")'
+RUN Rscript -e 'remotes::install_version("rmarkdown",upgrade="never", version = "2.3")'
+RUN Rscript -e 'remotes::install_version("shinydashboard",upgrade="never", version = "0.7.1")'
+RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.15")'
+RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.2.1")'
+RUN mkdir /build_zone
+ADD . /build_zone
+WORKDIR /build_zone
+RUN R -e 'remotes::install_local(upgrade="never")'
+EXPOSE 80
+CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');csbcPsonManifest::run_app()"

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(run_app)
+import(dccvalidator)
+import(dplyr)
+import(reticulate)
+import(shiny)
+import(shinyBS)
+import(shinydashboard)
+import(shinyjs)
+import(tibble)
+import(waiter)
+importFrom(config,get)
+importFrom(golem,activate_js)
+importFrom(golem,add_resource_path)
+importFrom(golem,bundle_resources)
+importFrom(golem,favicon)
+importFrom(golem,with_golem_options)
+importFrom(htmltools,HTML)
+importFrom(htmltools,tagAppendAttributes)
+importFrom(htmltools,tagList)
+importFrom(htmltools,tags)
+importFrom(shiny,NS)
+importFrom(shiny,column)
+importFrom(shiny,shinyApp)
+importFrom(shiny,tagList)

R/app_config.R

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+#' Access files in the current app
+#' 
+#' @param ... Character vector specifying directory and or file to
+#'     point to inside the current package.
+#' 
+#' @noRd
+app_sys <- function(...){
+  system.file(..., package = "csbcPsonManifest")
+}
+
+
+#' Read App Config
+#' 
+#' @param value Value to retrieve from the config file. 
+#' @param config R_CONFIG_ACTIVE value. 
+#' @param use_parent Logical, scan the parent directory for config file.
+#'     
+#' @importFrom config get
+#' 
+#' @noRd
+get_golem_config <- function(
+  value, 
+  config = Sys.getenv("R_CONFIG_ACTIVE", "default"), 
+  use_parent = TRUE
+){
+  config::get(
+    value = value, 
+    config = config, 
+    # Modify this if your config file is somewhere else:
+    file = app_sys("golem-config.yml"), 
+    use_parent = use_parent
+  )
+}
+

R/app_server.R

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+#' The application server-side
+#' 
+#' @param input,output,session Internal parameters for {shiny}. 
+#'     DO NOT REMOVE.
+#' @import shiny
+#' @import shinyjs
+#' @import shinydashboard
+#' @import shinyBS
+#' @import reticulate
+#' @import dplyr
+#' @import tibble
+#' @import waiter
+#' @import dccvalidator
+#' @noRd
+app_server <- function( input, output, session ) {
+  # List the first level callModules here
+  #Add synapse login
+  session$sendCustomMessage(type = "readCookie", message = list())
+  source_python("R/synapse_funcs.py")
+
+  syn <- .GlobalEnv$synapseclient$Synapse()
+  values <- reactiveValues()
+
+  observeEvent(input$cookie, {
+
+    if (input$cookie == "unauthorized") {
+      waiter::waiter_update(
+        html = tagList(
+          img(src = "www/synapse_logo.png",
+              height = "120px"),
+          h3("Looks like you're not logged in!"),
+          span("Please ", a("login", href = "https://www.synapse.org/#!LoginPlace:0", target = "_blank"),
+               " to Synapse, then refresh this page.")
+        )
+      )
+    } else {
+      ### login and update session; otherwise, notify to login to Synapse first
+      tryCatch({
+        syn$login(sessionToken = input$cookie)
+        values$tables <- get_tables(syn)
+        # get controlled-vocabulary list
+        values$cv_terms <- get_synapse_annotations("syn25322361", syn) %>%
+          select(key, value, columnType) %>%
+          unique()
+        ### update waiter loading screen once login successful
+        waiter::waiter_update(
+          html = tagList(
+            img(src = "www/synapse_logo.png",
+                height = "120px"),
+            h3(sprintf("Welcome, %s!", syn$getUserProfile()$userName))
+          )
+        )
+        Sys.sleep(2)
+        waiter::waiter_hide()
+      }, error = function(err) {
+        print(err)
+        Sys.sleep(2)
+        waiter::waiter_update(
+          html = tagList(
+            img(src = "www/synapse_logo.png", height = "120px"),
+            h3("Login error"),
+            span(
+              "There was an error with the login process. Please refresh your Synapse session by logging out of and back in to",
+              a("Synapse", href = "https://www.synapse.org/", target = "_blank"),
+              ", then refresh this page."
+            )
+          )
+        )
+
+      })
+
+    }
+    # output$title <- shiny::renderUI({
+    #   shiny::titlePanel(sprintf("Welcome, %s", syn$getUserProfile()$userName))
+    # })
+    shiny::callModule(mod_home_server, "home_ui_1", values)
+    shiny::callModule(mod_quickview_server, "quickview_ui_1", values)
+    shiny::callModule(mod_validator_server, "validator_ui_1", values)
+
+  })
+}