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Merge pull request #133 from FredHutch/dev
shiny-cromwell v1.1.0 Updates
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,14 +1,21 @@ | ||
| FROM fredhutch/r-shiny-server-base:4.3.2 | ||
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| RUN apt-get update -y && apt-get install -y libssh-dev | ||
| RUN apt-get update -y && apt-get install -y libssh-dev python3-pip git libmariadb-dev | ||
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| RUN R -q -e 'install.packages(c("ellipsis"), repos="https://cran.rstudio.com/")' | ||
| RUN R -q -e 'install.packages(c("shiny"), repos="https://cran.rstudio.com/")' | ||
| RUN R -q -e 'install.packages(c("shinyFeedback", "shinyWidgets", "shinydashboard", "shinydashboardPlus", "ssh", "remotes", "markdown", "lubridate", "jsonlite", "dplyr", "DT", "glue", "httr", "purrr", "RColorBrewer", "rlang", "shinyBS", "shinyjs", "tidyverse", "uuid", "memoise", "rclipboard", "shinyvalidate", "shinylogs", "testhat"), repos="https://cran.r-project.org")' | ||
| RUN R -q -e 'install.packages(c("shinyFeedback", "shinyWidgets", "shinydashboard", "shinydashboardPlus", "ssh", "remotes", "markdown", "lubridate", "jsonlite", "dplyr", "DT", "glue", "httr", "purrr", "RColorBrewer", "rlang", "shinyBS", "shinyjs", "tidyverse", "uuid", "memoise", "rclipboard", "shinyvalidate", "shinylogs", "testhat", "bsicons", "listviewer", "cookies", "RMariaDB", "DBI"), repos="https://cran.r-project.org")' | ||
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| RUN R -q -e "remotes::install_github('getwilds/proofr@v0.2')" | ||
| RUN R -q -e "remotes::install_github('getwilds/proofr@v0.3.0')" | ||
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| RUN R -q -e "remotes::install_github('getwilds/[email protected]')" | ||
| RUN R -q -e "remotes::install_github('getwilds/[email protected]')" | ||
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| ADD .my.cnf /root/ | ||
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| # python wdl2mermaid setup: | ||
| RUN pip install git+https://github.com/chanzuckerberg/miniwdl-viz.git | ||
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| RUN R -q -e "remotes::install_github('timelyportfolio/reactR')" | ||
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| RUN rm -rf /srv/shiny-server/ | ||
| COPY app/ /srv/shiny-server/ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| library(RMariaDB) | ||
| library(DBI) | ||
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| COOKIE_EXPIRY_DAYS <- 14 | ||
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| to_base64 <- function(x) { | ||
| base64enc::base64encode(charToRaw(x)) | ||
| } | ||
| from_base64 <- function(x) { | ||
| rawToChar(base64enc::base64decode(x)) | ||
| } | ||
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| db <- dbConnect(RMariaDB::MariaDB(), group = "shinycromwell") | ||
| if (!dbExistsTable(db, "users")) { | ||
| db_columns <- c( | ||
| user = "TEXT", | ||
| proof_token = "TEXT", | ||
| cromwell_url = "TEXT", | ||
| login_time = "TEXT" | ||
| ) | ||
| dbCreateTable(db, "users", db_columns) | ||
| } | ||
| dbDisconnect(db) | ||
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| make_db_con <- function() { | ||
| dbConnect(RMariaDB::MariaDB(), group = "shinycromwell") | ||
| } | ||
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| user_from_db <- function(user, conn = make_db_con(), expiry = COOKIE_EXPIRY_DAYS) { | ||
| on.exit(dbDisconnect(conn)) | ||
| dbReadTable(conn, "users") %>% | ||
| as_tibble() %>% | ||
| filter( | ||
| # !! needed to get the value of the variable | ||
| user == !!user, | ||
| login_time > now() - days(expiry) | ||
| ) %>% | ||
| arrange(desc(login_time)) | ||
| } | ||
| user_to_db <- function(user, token, url, drop_existing = FALSE, conn = make_db_con()) { | ||
| on.exit(dbDisconnect(conn)) | ||
| # drop before inserting so we only have 1 row/user | ||
| if (drop_existing) { | ||
| # don't drop if user is empty | ||
| if (nzchar(user)) { | ||
| # don't disconnect from within drop fun | ||
| user_drop_from_db(user, disconnect = FALSE, conn = conn) | ||
| } | ||
| } | ||
| tibble( | ||
| user = user, | ||
| proof_token = token, | ||
| cromwell_url = url, | ||
| login_time = as.character(now()) | ||
| ) %>% | ||
| dbWriteTable(conn, "users", ., append = TRUE) | ||
| } | ||
| user_drop_from_db <- function(user, disconnect = TRUE, conn = make_db_con()) { | ||
| if (disconnect) { | ||
| on.exit(dbDisconnect(conn)) | ||
| } | ||
| sql_delete <- glue::glue_sql(" | ||
| DELETE from users | ||
| WHERE user = {user} | ||
| ", .con = conn) | ||
| dbExecute(conn, sql_delete) | ||
| } |
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