tservice-plugins
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corrplot
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First Commit.

tags/v0.1.0
YJC 3 vuotta sitten
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  1. +11
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  2. +24
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  3. +277
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  4. +42
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  5. +3
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  6. +26
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  7. +1
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  8. +74
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      resources/corrplot/bin/corrplot.R
  9. +99
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      resources/corrplot/bin/corrplot.sh
  10. +22
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  11. +33
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  12. +626
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      resources/examples/result.json
  13. +468
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  15. +653
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      resources/renv/activate.R
  16. +7
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  17. +10
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      resources/templates/args.json.template
  18. +0
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      resources/templates/result.md.template
  19. +33
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      resources/tservice-plugin.yaml
  20. +142
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  21. +34
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      src/tservice/plugins/corrplot/common.clj
  22. +7
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      test/tservice/plugins/corrplot_test.clj

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/target
/classes
/checkouts
pom.xml
pom.xml.asc
*.jar
*.class
/.lein-*
/.nrepl-port
.hgignore
.hg/

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# Change Log
All notable changes to this project will be documented in this file. This change log follows the conventions of [keepachangelog.com](http://keepachangelog.com/).

## [Unreleased]
### Changed
- Add a new arity to `make-widget-async` to provide a different widget shape.

## [0.1.1] - 2021-05-27
### Changed
- Documentation on how to make the widgets.

### Removed
- `make-widget-sync` - we're all async, all the time.

### Fixed
- Fixed widget maker to keep working when daylight savings switches over.

## 0.1.0 - 2021-05-27
### Added
- Files from the new template.
- Widget maker public API - `make-widget-sync`.

[Unreleased]: https://github.com/your-name/corrplot/compare/0.1.1...HEAD
[0.1.1]: https://github.com/your-name/corrplot/compare/0.1.0...0.1.1

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# corrplot

FIXME: description

## Installation

Download from http://example.com/FIXME.

## Usage

FIXME: explanation

## Options

FIXME: listing of options this app accepts.

## Examples

...

### Bugs

...

### Any Other Sections
### That You Think
### Might be Useful

## License

Copyright © 2021 FIXME

This program and the accompanying materials are made available under the
terms of the Eclipse Public License 2.0 which is available at
http://www.eclipse.org/legal/epl-2.0.

This Source Code may also be made available under the following Secondary
Licenses when the conditions for such availability set forth in the Eclipse
Public License, v. 2.0 are satisfied: GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or (at your
option) any later version, with the GNU Classpath Exception which is available
at https://www.gnu.org/software/classpath/license.html.

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# Introduction to corrplot

TODO: write [great documentation](http://jacobian.org/writing/what-to-write/)

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project.clj Näytä tiedosto

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(defproject tservice-plugins/corrplot "v0.1.0"
:description "FIXME: write description"
:url "https://github.com/tservice-plugins/corrplot"
:license {:name "Eclipse Public License"
:url "http://www.eclipse.org/legal/epl-v10.html"}
:min-lein-version "2.5.0"
:deployable false

:dependencies
[[org.clojure/tools.logging "1.1.0"]
[selmer "1.12.27"]]

:profiles
{:provided
{:dependencies
[[org.clojure/clojure "1.10.1"]
[org.clojars.yjcyxky/tservice "0.6.0"]]}
:uberjar
{:auto-clean true
:aot :all
:omit-source true
:javac-options ["-target" "1.8", "-source" "1.8"]
:target-path "target/%s"
:resource-paths ["resources"]
:uberjar-name "corrplot.tservice-plugin.jar"}})

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source("renv/activate.R")

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#!/usr/bin/env Rscript

# For more information, please see https://plot.ly/r/shinyapp-explore-diamonds/
library(configr)
library(ggplot2)
library(plotly)
library(dplyr)
library(ggcorrplot)
library(RColorBrewer)

read_json <- function(jsonfile) {
return(read.config(jsonfile))
}

getColors <- function(n, dataType = "seq") {
allChoices <- brewer.pal.info

availableChoices <- allChoices[allChoices$maxcolors > n & allChoices$category == dataType,]

if (dim(availableChoices)[1] != 0) {
colorPal <- sample(rownames(availableChoices), size = 1)
if (n <= 3) {
options <- brewer.pal(3, colorPal)
return(options[1:n])
} else {
return(brewer.pal(n, colorPal))
}
} else {
return(NULL)
}
}

getLen <- function(x) {
return(length(unique(x)))
}

make_corrplot <- function(args_json) {
input <- read_json(args_json)
data <- read.csv(input$datafile)
colors <- getColors(3, "div")

result <- cor(data[, input$corr_vars])
# build graph with ggplot syntax
p <- ggcorrplot(result, method = input$method, type = input$corr_type,
show.diag = TRUE, colors = colors,
outline.col = "white", hc.order = input$hc_order,
hc.method = input$hc_method, lab = TRUE,
lab_col = "black", lab_size = 4, p.mat = NULL,
sig.level = input$sig_level, title = input$title,
show.legend = TRUE, legend.title = "", insig = "pch",
ggtheme = ggplot2::theme_gray, pch = 4, pch.col = "black") +
theme(axis.text.x = element_text(angle = 0, hjust = 1, margin = margin(-3, 0, 0, 0),
size = 11),
axis.text.y = element_text(size = 11,
margin = margin(0, -3, 0, 0)),
text = element_text(size = input$corrplot_title_size),
legend.text = element_text(size = 11),
legend.title = element_blank(),
panel.background = element_blank(),
panel.grid.major = element_blank(),
axis.line = element_line(colour = "black"))

return(ggplotly(p))
}

write_json <- function(plotly_object, output_file) {
json <- plotly::plotly_json(plotly_object, FALSE)
write(json, output_file)
}

corrplot <- function(args_json, output_file) {
plotly_object <- make_corrplot(args_json)
write_json(plotly_object, output_file)
}

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#!/usr/bin/env bash

# A wrapper for corrplot r function
#
# Author: Jingcheng Yang
# Email: yjcyxky@163.com
#
# License: MIT

# Exit on error. Append "|| true" if you expect an error.
# set -o errexit
# Exit on error inside any functions or subshells.
# set -o errtrace
# Do not allow use of undefined vars. Use ${VAR:-} to use an undefined VAR
set -o nounset
# Catch the error in case mysqldump fails (but gzip succeeds) in `mysqldump |gzip`
set -o pipefail
# Turn on traces, useful while debugging but commented out by default
# set -o xtrace

show_help() {
cat <<EOF
usage: $(echo $0) [-d <INPUT_FILE>] [-o <OUTPUT_FILE>]
-i INPUT_FILE An argument json file.
-o OUTPUT_FILE A plotly json file.
EOF
}

while getopts ":hi:o:" arg; do
case "$arg" in
"i")
INPUT_FILE="$OPTARG"
;;
"o")
OUTPUT_FILE="$OPTARG"
;;
"?")
echo "Unkown option: $OPTARG"
exit 1
;;
":")
echo "No argument value for option $OPTARG"
;;
h)
show_help
exit 0
;;
*)
echo "Unknown error while processing options"
show_help
exit 1
;;
esac
done

if [ -z "$INPUT_FILE" ]; then
echo "-i argument is not specified."
exit 1
elif [ ! -f "$INPUT_FILE" ]; then
echo "$INPUT_FILE is not a valid file."
exit 1
else
INPUT_FILE=$(realpath $INPUT_FILE)
fi

if [ -z "$OUTPUT_FILE" ]; then
echo "-o argument is not specified."
exit 1
elif [ ! -f "$OUTPUT_FILE" ]; then
echo "$OUTPUT_FILE is not a valid file."
exit 1
else
OUTPUT_FILE=$(realpath $OUTPUT_FILE)
fi

TEMP=$(mktemp)

echo "Run script: $TEMP"

SCRIPT_DIR=`realpath $(dirname $0)`

cat <<EOF >"$TEMP"
#!/usr/bin/env Rscript

run <- function() {
# Print traceback message
on.exit(traceback())
source("${SCRIPT_DIR}/corrplot.R")
corrplot("${INPUT_FILE}", "${OUTPUT_FILE}")
}

run()
EOF

printf "\n---------------------\n"
cat "$TEMP"
echo "---------------------"

Rscript $TEMP

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{
"datafile": "./examples/data.csv",
"corr_vars": [
"mpg",
"cyl",
"disp",
"hp",
"drat",
"wt",
"qsec",
"vs",
"am",
"gear",
"carb"
],
"method": "square",
"corr_type": "full",
"hc_method": "complete",
"hc_order": true,
"sig_level": 0.05,
"title": "This is a test."
}

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name,mpg,cyl,disp,hp,drat,wt,qsec,vs,am,gear,carb
Mazda RX4,21,6,160,110,3.9,2.62,16.46,0,1,4,4
Mazda RX4 Wag,21,6,160,110,3.9,2.875,17.02,0,1,4,4
Datsun 710,22.8,4,108,93,3.85,2.32,18.61,1,1,4,1
Hornet 4 Drive,21.4,6,258,110,3.08,3.215,19.44,1,0,3,1
Hornet Sportabout,18.7,8,360,175,3.15,3.44,17.02,0,0,3,2
Valiant,18.1,6,225,105,2.76,3.46,20.22,1,0,3,1
Duster 360,14.3,8,360,245,3.21,3.57,15.84,0,0,3,4
Merc 240D,24.4,4,146.7,62,3.69,3.19,20,1,0,4,2
Merc 230,22.8,4,140.8,95,3.92,3.15,22.9,1,0,4,2
Merc 280,19.2,6,167.6,123,3.92,3.44,18.3,1,0,4,4
Merc 280C,17.8,6,167.6,123,3.92,3.44,18.9,1,0,4,4
Merc 450SE,16.4,8,275.8,180,3.07,4.07,17.4,0,0,3,3
Merc 450SL,17.3,8,275.8,180,3.07,3.73,17.6,0,0,3,3
Merc 450SLC,15.2,8,275.8,180,3.07,3.78,18,0,0,3,3
Cadillac Fleetwood,10.4,8,472,205,2.93,5.25,17.98,0,0,3,4
Lincoln Continental,10.4,8,460,215,3,5.424,17.82,0,0,3,4
Chrysler Imperial,14.7,8,440,230,3.23,5.345,17.42,0,0,3,4
Fiat 128,32.4,4,78.7,66,4.08,2.2,19.47,1,1,4,1
Honda Civic,30.4,4,75.7,52,4.93,1.615,18.52,1,1,4,2
Toyota Corolla,33.9,4,71.1,65,4.22,1.835,19.9,1,1,4,1
Toyota Corona,21.5,4,120.1,97,3.7,2.465,20.01,1,0,3,1
Dodge Challenger,15.5,8,318,150,2.76,3.52,16.87,0,0,3,2
AMC Javelin,15.2,8,304,150,3.15,3.435,17.3,0,0,3,2
Camaro Z28,13.3,8,350,245,3.73,3.84,15.41,0,0,3,4
Pontiac Firebird,19.2,8,400,175,3.08,3.845,17.05,0,0,3,2
Fiat X1-9,27.3,4,79,66,4.08,1.935,18.9,1,1,4,1
Porsche 914-2,26,4,120.3,91,4.43,2.14,16.7,0,1,5,2
Lotus Europa,30.4,4,95.1,113,3.77,1.513,16.9,1,1,5,2
Ford Pantera L,15.8,8,351,264,4.22,3.17,14.5,0,1,5,4
Ferrari Dino,19.7,6,145,175,3.62,2.77,15.5,0,1,5,6
Maserati Bora,15,8,301,335,3.54,3.57,14.6,0,1,5,8
Volvo 142E,21.4,4,121,109,4.11,2.78,18.6,1,1,4,2

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{
"R": {
"Version": "3.6.3",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://cloud.r-project.org"
}
]
},
"Packages": {
"MASS": {
"Package": "MASS",
"Version": "7.3-51.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9efe80472b21189ebab1b74169808c26"
},
"Matrix": {
"Package": "Matrix",
"Version": "1.2-18",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "08588806cba69f04797dab50627428ed"
},
"R6": {
"Package": "R6",
"Version": "2.5.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "470851b6d5d0ac559e9d01bb352b4021"
},
"RColorBrewer": {
"Package": "RColorBrewer",
"Version": "1.1-2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e031418365a7f7a766181ab5a41a5716"
},
"Rcpp": {
"Package": "Rcpp",
"Version": "1.0.7",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "dab19adae4440ae55aa8a9d238b246bb"
},
"RcppTOML": {
"Package": "RcppTOML",
"Version": "0.1.7",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f8a578aa91321ecec1292f1e2ffadeda"
},
"askpass": {
"Package": "askpass",
"Version": "1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e8a22846fff485f0be3770c2da758713"
},
"base64enc": {
"Package": "base64enc",
"Version": "0.1-3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "543776ae6848fde2f48ff3816d0628bc"
},
"cli": {
"Package": "cli",
"Version": "3.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e3ae5d68dea0c55a12ea12a9fda02e61"
},
"colorspace": {
"Package": "colorspace",
"Version": "2.0-2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6baccb763ee83c0bd313460fdb8b8a84"
},
"configr": {
"Package": "configr",
"Version": "0.3.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "27bf543086066d25a38ed9fe26fa2ad8"
},
"cpp11": {
"Package": "cpp11",
"Version": "0.4.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "40ba3fd26c8f61d8d14d334bc7761df9"
},
"crayon": {
"Package": "crayon",
"Version": "1.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e75525c55c70e5f4f78c9960a4b402e9"
},
"crosstalk": {
"Package": "crosstalk",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2b06f9e415a62b6762e4b8098d2aecbc"
},
"curl": {
"Package": "curl",
"Version": "4.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "022c42d49c28e95d69ca60446dbabf88"
},
"data.table": {
"Package": "data.table",
"Version": "1.14.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "36b67b5adf57b292923f5659f5f0c853"
},
"digest": {
"Package": "digest",
"Version": "0.6.28",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "49b5c6e230bfec487b8917d5a0c77cca"
},
"dplyr": {
"Package": "dplyr",
"Version": "1.0.7",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "36f1ae62f026c8ba9f9b5c9a08c03297"
},
"ellipsis": {
"Package": "ellipsis",
"Version": "0.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
},
"fansi": {
"Package": "fansi",
"Version": "0.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d447b40982c576a72b779f0a3b3da227"
},
"farver": {
"Package": "farver",
"Version": "2.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "c98eb5133d9cb9e1622b8691487f11bb"
},
"fastmap": {
"Package": "fastmap",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "77bd60a6157420d4ffa93b27cf6a58b8"
},
"generics": {
"Package": "generics",
"Version": "0.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4d243a9c10b00589889fe32314ffd902"
},
"ggcorrplot": {
"Package": "ggcorrplot",
"Version": "0.1.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5d6f67b947e0962cf93208f139acd475"
},
"ggplot2": {
"Package": "ggplot2",
"Version": "3.3.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d7566c471c7b17e095dd023b9ef155ad"
},
"glue": {
"Package": "glue",
"Version": "1.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6efd734b14c6471cfe443345f3e35e29"
},
"gtable": {
"Package": "gtable",
"Version": "0.3.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ac5c6baf7822ce8732b343f14c072c4d"
},
"htmltools": {
"Package": "htmltools",
"Version": "0.5.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "526c484233f42522278ab06fb185cb26"
},
"htmlwidgets": {
"Package": "htmlwidgets",
"Version": "1.5.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "76147821cd3fcd8c4b04e1ef0498e7fb"
},
"httr": {
"Package": "httr",
"Version": "1.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a525aba14184fec243f9eaec62fbed43"
},
"ini": {
"Package": "ini",
"Version": "0.3.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6154ec2223172bce8162d4153cda21f7"
},
"isoband": {
"Package": "isoband",
"Version": "0.2.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7ab57a6de7f48a8dc84910d1eca42883"
},
"jsonlite": {
"Package": "jsonlite",
"Version": "1.7.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "98138e0994d41508c7a6b84a0600cfcb"
},
"labeling": {
"Package": "labeling",
"Version": "0.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "3d5108641f47470611a32d0bdf357a72"
},
"later": {
"Package": "later",
"Version": "1.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b61890ae77fea19fc8acadd25db70aa4"
},
"lattice": {
"Package": "lattice",
"Version": "0.20-38",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "848f8c593fd1050371042d18d152e3d7"
},
"lazyeval": {
"Package": "lazyeval",
"Version": "0.2.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d908914ae53b04d4c0c0fd72ecc35370"
},
"lifecycle": {
"Package": "lifecycle",
"Version": "1.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a6b6d352e3ed897373ab19d8395c98d0"
},
"magrittr": {
"Package": "magrittr",
"Version": "2.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "41287f1ac7d28a92f0a286ed507928d3"
},
"mgcv": {
"Package": "mgcv",
"Version": "1.8-31",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4bb7e0c4f3557583e1e8d3c9ffb8ba5c"
},
"mime": {
"Package": "mime",
"Version": "0.11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "8974a907200fc9948d636fe7d85ca9fb"
},
"munsell": {
"Package": "munsell",
"Version": "0.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6dfe8bf774944bd5595785e3229d8771"
},
"nlme": {
"Package": "nlme",
"Version": "3.1-144",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e80d41932d3cc235ccbbbb9732ae162e"
},
"openssl": {
"Package": "openssl",
"Version": "1.4.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5406fd37ef0bf9b88c8a4f264d6ec220"
},
"pillar": {
"Package": "pillar",
"Version": "1.6.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "3323bc1a0988d63b5c65771ba0d3935d"
},
"pkgconfig": {
"Package": "pkgconfig",
"Version": "2.0.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "01f28d4278f15c76cddbea05899c5d6f"
},
"plotly": {
"Package": "plotly",
"Version": "4.9.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "af4b92cb3828aa30002e2f945c49c2d7"
},
"plyr": {
"Package": "plyr",
"Version": "1.8.6",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ec0e5ab4e5f851f6ef32cd1d1984957f"
},
"promises": {
"Package": "promises",
"Version": "1.2.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4ab2c43adb4d4699cf3690acd378d75d"
},
"purrr": {
"Package": "purrr",
"Version": "0.3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "97def703420c8ab10d8f0e6c72101e02"
},
"renv": {
"Package": "renv",
"Version": "0.13.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9f10d9db5b50400c348920c5c603385e"
},
"reshape2": {
"Package": "reshape2",
"Version": "1.4.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "bb5996d0bd962d214a11140d77589917"
},
"rlang": {
"Package": "rlang",
"Version": "0.4.11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "515f341d3affe0de9e4a7f762efb0456"
},
"scales": {
"Package": "scales",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6f76f71042411426ec8df6c54f34e6dd"
},
"stringi": {
"Package": "stringi",
"Version": "1.7.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ebaccb577da50829a3bb1b8296f318a5"
},
"stringr": {
"Package": "stringr",
"Version": "1.4.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0759e6b6c0957edb1311028a49a35e76"
},
"sys": {
"Package": "sys",
"Version": "3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b227d13e29222b4574486cfcbde077fa"
},
"tibble": {
"Package": "tibble",
"Version": "3.1.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5e8ad5621e5c94b24ec07b88eee13df8"
},
"tidyr": {
"Package": "tidyr",
"Version": "1.1.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "c8fbdbd9fcac223d6c6fe8e406f368e1"
},
"tidyselect": {
"Package": "tidyselect",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7243004a708d06d4716717fa1ff5b2fe"
},
"utf8": {
"Package": "utf8",
"Version": "1.2.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "c9c462b759a5cc844ae25b5942654d13"
},
"vctrs": {
"Package": "vctrs",
"Version": "0.3.8",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ecf749a1b39ea72bd9b51b76292261f1"
},
"viridisLite": {
"Package": "viridisLite",
"Version": "0.4.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "55e157e2aa88161bdb0754218470d204"
},
"withr": {
"Package": "withr",
"Version": "2.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ad03909b44677f930fa156d47d7a3aeb"
},
"yaml": {
"Package": "yaml",
"Version": "2.2.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2826c5d9efb0a88f657c7a679c7106db"
}
}
}

+ 5
- 0
resources/renv/.gitignore Näytä tiedosto

@@ -0,0 +1,5 @@
library/
local/
lock/
python/
staging/

+ 653
- 0
resources/renv/activate.R Näytä tiedosto

@@ -0,0 +1,653 @@

local({

# the requested version of renv
version <- "0.13.0"

# the project directory
project <- getwd()

# avoid recursion
if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA)))
return(invisible(TRUE))

# signal that we're loading renv during R startup
Sys.setenv("RENV_R_INITIALIZING" = "true")
on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE)

# signal that we've consented to use renv
options(renv.consent = TRUE)

# load the 'utils' package eagerly -- this ensures that renv shims, which
# mask 'utils' packages, will come first on the search path
library(utils, lib.loc = .Library)

# check to see if renv has already been loaded
if ("renv" %in% loadedNamespaces()) {

# if renv has already been loaded, and it's the requested version of renv,
# nothing to do
spec <- .getNamespaceInfo(.getNamespace("renv"), "spec")
if (identical(spec[["version"]], version))
return(invisible(TRUE))

# otherwise, unload and attempt to load the correct version of renv
unloadNamespace("renv")

}

# load bootstrap tools
bootstrap <- function(version, library) {
# attempt to download renv
tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
if (inherits(tarball, "error"))
stop("failed to download renv ", version)
# now attempt to install
status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity)
if (inherits(status, "error"))
stop("failed to install renv ", version)
}
renv_bootstrap_tests_running <- function() {
getOption("renv.tests.running", default = FALSE)
}
renv_bootstrap_repos <- function() {
# check for repos override
repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
if (!is.na(repos))
return(repos)
# if we're testing, re-use the test repositories
if (renv_bootstrap_tests_running())
return(getOption("renv.tests.repos"))
# retrieve current repos
repos <- getOption("repos")
# ensure @CRAN@ entries are resolved
repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
# add in renv.bootstrap.repos if set
default <- c(FALLBACK = "https://cloud.r-project.org")
extra <- getOption("renv.bootstrap.repos", default = default)
repos <- c(repos, extra)
# remove duplicates that might've snuck in
dupes <- duplicated(repos) | duplicated(names(repos))
repos[!dupes]
}
renv_bootstrap_download <- function(version) {
# if the renv version number has 4 components, assume it must
# be retrieved via github
nv <- numeric_version(version)
components <- unclass(nv)[[1]]
methods <- if (length(components) == 4L) {
list(
renv_bootstrap_download_github
)
} else {
list(
renv_bootstrap_download_cran_latest,
renv_bootstrap_download_cran_archive
)
}
for (method in methods) {
path <- tryCatch(method(version), error = identity)
if (is.character(path) && file.exists(path))
return(path)
}
stop("failed to download renv ", version)
}
renv_bootstrap_download_impl <- function(url, destfile) {
mode <- "wb"
# https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
fixup <-
Sys.info()[["sysname"]] == "Windows" &&
substring(url, 1L, 5L) == "file:"
if (fixup)
mode <- "w+b"
utils::download.file(
url = url,
destfile = destfile,
mode = mode,
quiet = TRUE
)
}
renv_bootstrap_download_cran_latest <- function(version) {
repos <- renv_bootstrap_download_cran_latest_find(version)
message("* Downloading renv ", version, " ... ", appendLF = FALSE)
downloader <- function(type) {
tryCatch(
utils::download.packages(
pkgs = "renv",
destdir = tempdir(),
repos = repos,
type = type,
quiet = TRUE
),
condition = identity
)
}
# first, try downloading a binary on Windows + macOS if appropriate
binary <-
!identical(.Platform$pkgType, "source") &&
!identical(getOption("pkgType"), "source") &&
Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
if (binary) {
info <- downloader(type = "binary")
if (!inherits(info, "condition")) {
message("OK (downloaded binary)")
return(info[1, 2])
}
}
# otherwise, try downloading a source tarball
info <- downloader(type = "source")
if (inherits(info, "condition")) {
message("FAILED")
return(FALSE)
}
# report success and return
message("OK (downloaded source)")
info[1, 2]
}
renv_bootstrap_download_cran_latest_find <- function(version) {
all <- renv_bootstrap_repos()
for (repos in all) {
db <- tryCatch(
as.data.frame(
x = utils::available.packages(repos = repos),
stringsAsFactors = FALSE
),
error = identity
)
if (inherits(db, "error"))
next
entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
if (nrow(entry) == 0)
next
return(repos)
}
fmt <- "renv %s is not available from your declared package repositories"
stop(sprintf(fmt, version))
}
renv_bootstrap_download_cran_archive <- function(version) {
name <- sprintf("renv_%s.tar.gz", version)
repos <- renv_bootstrap_repos()
urls <- file.path(repos, "src/contrib/Archive/renv", name)
destfile <- file.path(tempdir(), name)
message("* Downloading renv ", version, " ... ", appendLF = FALSE)
for (url in urls) {
status <- tryCatch(
renv_bootstrap_download_impl(url, destfile),
condition = identity
)
if (identical(status, 0L)) {
message("OK")
return(destfile)
}
}
message("FAILED")
return(FALSE)
}
renv_bootstrap_download_github <- function(version) {
enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
if (!identical(enabled, "TRUE"))
return(FALSE)
# prepare download options
pat <- Sys.getenv("GITHUB_PAT")
if (nzchar(Sys.which("curl")) && nzchar(pat)) {
fmt <- "--location --fail --header \"Authorization: token %s\""
extra <- sprintf(fmt, pat)
saved <- options("download.file.method", "download.file.extra")
options(download.file.method = "curl", download.file.extra = extra)
on.exit(do.call(base::options, saved), add = TRUE)
} else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
fmt <- "--header=\"Authorization: token %s\""
extra <- sprintf(fmt, pat)
saved <- options("download.file.method", "download.file.extra")
options(download.file.method = "wget", download.file.extra = extra)
on.exit(do.call(base::options, saved), add = TRUE)
}
message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE)
url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
name <- sprintf("renv_%s.tar.gz", version)
destfile <- file.path(tempdir(), name)
status <- tryCatch(
renv_bootstrap_download_impl(url, destfile),
condition = identity
)
if (!identical(status, 0L)) {
message("FAILED")
return(FALSE)
}
message("OK")
return(destfile)
}
renv_bootstrap_install <- function(version, tarball, library) {
# attempt to install it into project library
message("* Installing renv ", version, " ... ", appendLF = FALSE)
dir.create(library, showWarnings = FALSE, recursive = TRUE)
# invoke using system2 so we can capture and report output
bin <- R.home("bin")
exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
r <- file.path(bin, exe)
args <- c("--vanilla", "CMD", "INSTALL", "-l", shQuote(library), shQuote(tarball))
output <- system2(r, args, stdout = TRUE, stderr = TRUE)
message("Done!")
# check for successful install
status <- attr(output, "status")
if (is.numeric(status) && !identical(status, 0L)) {
header <- "Error installing renv:"
lines <- paste(rep.int("=", nchar(header)), collapse = "")
text <- c(header, lines, output)
writeLines(text, con = stderr())
}
status
}
renv_bootstrap_platform_prefix <- function() {
# construct version prefix
version <- paste(R.version$major, R.version$minor, sep = ".")
prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
# include SVN revision for development versions of R
# (to avoid sharing platform-specific artefacts with released versions of R)
devel <-
identical(R.version[["status"]], "Under development (unstable)") ||
identical(R.version[["nickname"]], "Unsuffered Consequences")
if (devel)
prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
# build list of path components
components <- c(prefix, R.version$platform)
# include prefix if provided by user
prefix <- renv_bootstrap_platform_prefix_impl()
if (!is.na(prefix) && nzchar(prefix))
components <- c(prefix, components)
# build prefix
paste(components, collapse = "/")
}
renv_bootstrap_platform_prefix_impl <- function() {
# if an explicit prefix has been supplied, use it
prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
if (!is.na(prefix))
return(prefix)
# if the user has requested an automatic prefix, generate it
auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
if (auto %in% c("TRUE", "True", "true", "1"))
return(renv_bootstrap_platform_prefix_auto())
# empty string on failure
""
}
renv_bootstrap_platform_prefix_auto <- function() {
prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
if (inherits(prefix, "error") || prefix %in% "unknown") {
msg <- paste(
"failed to infer current operating system",
"please file a bug report at https://github.com/rstudio/renv/issues",
sep = "; "
)
warning(msg)
}
prefix
}
renv_bootstrap_platform_os <- function() {
sysinfo <- Sys.info()
sysname <- sysinfo[["sysname"]]
# handle Windows + macOS up front
if (sysname == "Windows")
return("windows")
else if (sysname == "Darwin")
return("macos")
# check for os-release files
for (file in c("/etc/os-release", "/usr/lib/os-release"))
if (file.exists(file))
return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
# check for redhat-release files
if (file.exists("/etc/redhat-release"))
return(renv_bootstrap_platform_os_via_redhat_release())
"unknown"
}
renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
# read /etc/os-release
release <- utils::read.table(
file = file,
sep = "=",
quote = c("\"", "'"),
col.names = c("Key", "Value"),
comment.char = "#",
stringsAsFactors = FALSE
)
vars <- as.list(release$Value)
names(vars) <- release$Key
# get os name
os <- tolower(sysinfo[["sysname"]])
# read id
id <- "unknown"
for (field in c("ID", "ID_LIKE")) {
if (field %in% names(vars) && nzchar(vars[[field]])) {
id <- vars[[field]]
break
}
}
# read version
version <- "unknown"
for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
if (field %in% names(vars) && nzchar(vars[[field]])) {
version <- vars[[field]]
break
}
}
# join together
paste(c(os, id, version), collapse = "-")
}
renv_bootstrap_platform_os_via_redhat_release <- function() {
# read /etc/redhat-release
contents <- readLines("/etc/redhat-release", warn = FALSE)
# infer id
id <- if (grepl("centos", contents, ignore.case = TRUE))
"centos"
else if (grepl("redhat", contents, ignore.case = TRUE))
"redhat"
else
"unknown"
# try to find a version component (very hacky)
version <- "unknown"
parts <- strsplit(contents, "[[:space:]]")[[1L]]
for (part in parts) {
nv <- tryCatch(numeric_version(part), error = identity)
if (inherits(nv, "error"))
next
version <- nv[1, 1]
break
}
paste(c("linux", id, version), collapse = "-")
}
renv_bootstrap_library_root_name <- function(project) {
# use project name as-is if requested
asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
if (asis)
return(basename(project))
# otherwise, disambiguate based on project's path
id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
paste(basename(project), id, sep = "-")
}
renv_bootstrap_library_root <- function(project) {
path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
if (!is.na(path))
return(path)
path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
if (!is.na(path)) {
name <- renv_bootstrap_library_root_name(project)
return(file.path(path, name))
}
prefix <- renv_bootstrap_profile_prefix()
paste(c(project, prefix, "renv/library"), collapse = "/")
}
renv_bootstrap_validate_version <- function(version) {
loadedversion <- utils::packageDescription("renv", fields = "Version")
if (version == loadedversion)
return(TRUE)
# assume four-component versions are from GitHub; three-component
# versions are from CRAN
components <- strsplit(loadedversion, "[.-]")[[1]]
remote <- if (length(components) == 4L)
paste("rstudio/renv", loadedversion, sep = "@")
else
paste("renv", loadedversion, sep = "@")
fmt <- paste(
"renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
"Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
"Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
sep = "\n"
)
msg <- sprintf(fmt, loadedversion, version, remote)
warning(msg, call. = FALSE)
FALSE
}
renv_bootstrap_hash_text <- function(text) {
hashfile <- tempfile("renv-hash-")
on.exit(unlink(hashfile), add = TRUE)
writeLines(text, con = hashfile)
tools::md5sum(hashfile)
}
renv_bootstrap_load <- function(project, libpath, version) {
# try to load renv from the project library
if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
return(FALSE)
# warn if the version of renv loaded does not match
renv_bootstrap_validate_version(version)
# load the project
renv::load(project)
TRUE
}
renv_bootstrap_profile_load <- function(project) {
# if RENV_PROFILE is already set, just use that
profile <- Sys.getenv("RENV_PROFILE", unset = NA)
if (!is.na(profile) && nzchar(profile))
return(profile)
# check for a profile file (nothing to do if it doesn't exist)
path <- file.path(project, "renv/local/profile")
if (!file.exists(path))
return(NULL)
# read the profile, and set it if it exists
contents <- readLines(path, warn = FALSE)
if (length(contents) == 0L)
return(NULL)
# set RENV_PROFILE
profile <- contents[[1L]]
if (nzchar(profile))
Sys.setenv(RENV_PROFILE = profile)
profile
}
renv_bootstrap_profile_prefix <- function() {
profile <- renv_bootstrap_profile_get()
if (!is.null(profile))
return(file.path("renv/profiles", profile))
}
renv_bootstrap_profile_get <- function() {
profile <- Sys.getenv("RENV_PROFILE", unset = "")
renv_bootstrap_profile_normalize(profile)
}
renv_bootstrap_profile_set <- function(profile) {
profile <- renv_bootstrap_profile_normalize(profile)
if (is.null(profile))
Sys.unsetenv("RENV_PROFILE")
else
Sys.setenv(RENV_PROFILE = profile)
}
renv_bootstrap_profile_normalize <- function(profile) {
if (is.null(profile) || profile %in% c("", "default"))
return(NULL)
profile
}

# load the renv profile, if any
renv_bootstrap_profile_load(project)

# construct path to library root
root <- renv_bootstrap_library_root(project)

# construct library prefix for platform
prefix <- renv_bootstrap_platform_prefix()

# construct full libpath
libpath <- file.path(root, prefix)

# attempt to load
if (renv_bootstrap_load(project, libpath, version))
return(TRUE)

# load failed; inform user we're about to bootstrap
prefix <- paste("# Bootstrapping renv", version)
postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "")
header <- paste(prefix, postfix)
message(header)

# perform bootstrap
bootstrap(version, libpath)

# exit early if we're just testing bootstrap
if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
return(TRUE)

# try again to load
if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
message("* Successfully installed and loaded renv ", version, ".")
return(renv::load())
}

# failed to download or load renv; warn the user
msg <- c(
"Failed to find an renv installation: the project will not be loaded.",
"Use `renv::activate()` to re-initialize the project."
)

warning(paste(msg, collapse = "\n"), call. = FALSE)

})

+ 7
- 0
resources/renv/settings.dcf Näytä tiedosto

@@ -0,0 +1,7 @@
external.libraries:
ignored.packages:
package.dependency.fields: Imports, Depends, LinkingTo
r.version:
snapshot.type: implicit
use.cache: TRUE
vcs.ignore.library: TRUE

+ 10
- 0
resources/templates/args.json.template Näytä tiedosto

@@ -0,0 +1,10 @@
{
"datafile": "{{ datafile }}",
"corr_vars": {{ corr_vars }},
"method": "{{ method | default: "square" }}",
"corr_type": "{{ corr_type | default: "full" }}",
"hc_method": "{{ hc_method | default: "complete" }}",
"hc_order": {{ hc_order }},
"sig_level": {{ sig_level | default: 0.05 }},
"title": "{{ title | default: "This is a correlation plot" }}"
}

+ 0
- 0
resources/templates/result.md.template Näytä tiedosto


+ 33
- 0
resources/tservice-plugin.yaml Näytä tiedosto

@@ -0,0 +1,33 @@
info:
name: Correlation Plot
version: v0.1.0
description: It is used to investigate the dependence between multiple variables at the same time and to highlight the most correlated variables in a data table.
category: Chart
home: https://github.com/tservice-plugins/corrplot
source: PGx
short_name: corrplot
icons:
- src: ""
type: image/png
sizes: 192x192
author: Jingcheng Yang
plugin:
name: corrplot
display-name: Correlation Plot
lazy-load: false
init:
- step: unpack-env
envname: corrplot
envtype: environment
- step: unpack-env
envname: templates
envtype: configuration
- step: unpack-env
envname: examples
envtype: data
- step: load-namespace
namespace: tservice.plugins.corrplot
- step: register-plugin
entrypoint: tservice.plugins.corrplot/metadata
- step: init-event
entrypoint: tservice.plugins.corrplot/events-init

+ 142
- 0
src/tservice/plugins/corrplot.clj Näytä tiedosto

@@ -0,0 +1,142 @@
(ns tservice.plugins.corrplot
(:require [clojure.data.json :as json]
[clojure.spec.alpha :as s]
[clojure.tools.logging :as log]
[spec-tools.core :as st]
[tservice.util :as u]
[tservice.lib.files :as ff]
[tservice.lib.fs :as fs-lib]
[tservice.plugins.corrplot.common :as corrplot]
[tservice.api.task :refer [publish-event! make-plugin-metadata make-events-init create-task! update-process!]]))

;;; ------------------------------------------------ Event Specs ------------------------------------------------
(s/def ::datafile
(st/spec
{:spec string?
:type :string
:description "A path for data file."
:swagger/default ""
:reason "The datafile must be string."}))

(s/def ::corr_vars
(st/spec
{:spec vector?
:type :vector
:description "Variables."
:swagger/default []
:reason "The corr_vars must be a vector."}))

(s/def ::method
(st/spec
{:spec #{"square" "circle"}
:type :string
:description "The visualization method of correlation matrix to be used. Allowed values are square (default), circle."
:swagger/default "square"
:reason "The corr_vars must be a vector."}))

(s/def ::corr_type
(st/spec
{:spec #{"full" "lower" "upper"}
:type :string
:description "full (default), lower or upper display."
:swagger/default "full"
:reason "The corr_type must be one of full, lower, upper."}))

(s/def ::hc_method
(st/spec
{:spec #{"ward.D" "ward.D2" "single" "complete" "average" "mcquitty" "median" "centroid"}
:type :string
:description "The agglomeration method to be used in hclust (see ?hclust)."
:swagger/default "complete"
:reason "The hc_method must be (an unambiguous abbreviation of) one of ward.D, ward.D2,
single, complete, average, mcquitty, median or centroid."}))

(s/def ::hc_order
(st/spec
{:spec #{true false}
:type :boolean
:description "Logical value. If TRUE, correlation matrix will be hc.ordered using hclust function."
:swagger/default true
:reason "The hc_order must be one of true, false."}))

(s/def ::sig_level
(st/spec
{:spec #(and (>= % 0) (<= % 1))
:type :float
:description "Logical value. If TRUE, correlation matrix will be hc.ordered using hclust function."
:swagger/default 0.05
:reason "The hc_order must be one of true, false."}))

(def corrplot-params-body
"A spec for the body parameters."
(s/keys :req-un [::datafile ::corr_vars]
:opt-un [::sig_level ::hc_order ::hc_method ::corr_type ::method]))

;;; ------------------------------------------------ Event Metadata ------------------------------------------------
(def metadata
(make-plugin-metadata
{:name "corrplot"
:summary "It is used to investigate the dependence between multiple variables at the same time and to highlight the most correlated variables in a data table."
:params-schema corrplot-params-body
:handler (fn [{:keys [datafile corr_vars sig_level hc_order hc_method corr_type method plugin-env]
:or {sig_level 0.05
hc_order true
hc_method "complete"
corr_type "full"
method "square"}
:as payload}]
(log/info "Make a correlation plot with %s" payload)
(let [workdir (ff/get-workdir)
log-path (fs-lib/join-paths workdir "log")
response {:files [(fs-lib/join-paths workdir "plotly.json")
(fs-lib/join-paths workdir "result.md")]
:log log-path
:response-type :data2files}
task-id (create-task! {:name (str "corrplot" (u/datetime))
:description "Make a correlation plot."
:payload payload
:plugin-name (:plugin-name plugin-env)
:plugin-type (:plugin-type plugin-env)
:plugin-version (:plugin-version plugin-env)
:response response})]
(fs-lib/create-directories! workdir)
(spit log-path (json/write-str {:status "Running" :msg ""}))
(update-process! task-id 0)
(publish-event! "corrplot"
{:context {:datafile datafile
:corr_vars corr_vars
:sig_level sig_level
:hc_order hc_order
:hc_method hc_method
:corr_type corr_type
:method method
:title "Correlation Plot"}
:template-dir (fs-lib/join-paths (:config-dir plugin-env) "templates")
:env-dir (:env-dir plugin-env)
:dest-dir workdir
:task-id task-id})
response))
:plugin-type :ChartPlugin
:response-type :data2files}))

;;; ------------------------------------------------ Event Processing ------------------------------------------------
(defn- corrplot!
"Make a correlation plot"
[{:keys [context dest-dir template-dir env-dir task-id]}]
(let [log-path (fs-lib/join-paths dest-dir "log")
args-json (fs-lib/join-paths dest-dir "arguments.json")
args-template (fs-lib/join-paths template-dir "args.json.template")
output-file (fs-lib/join-paths dest-dir "plotly.json")]
(corrplot/make-args-json! args-template context args-json)
(log/info "Make an argument json file: %s" args-json)
(update-process! task-id 30)
(let [result (corrplot/call-corrplot! args-json output-file env-dir)
status (:status result)]
(spit log-path (json/write-str result))
(log/info "The task is finished, result file is %s" output-file)
(update-process! task-id (if (= status "Success") 100 -1)))))

;;; --------------------------------------------------- Lifecycle ----------------------------------------------------
(def events-init
"Automatically called during startup; start event listener for corrplot events."
(make-events-init "corrplot" corrplot!))

+ 34
- 0
src/tservice/plugins/corrplot/common.clj Näytä tiedosto

@@ -0,0 +1,34 @@
(ns tservice.plugins.corrplot.common
(:require [selmer.parser :as parser]
[tservice.lib.files :refer [get-path-variable]]
[clojure.java.shell :as shell :refer [sh]]
[tservice.lib.fs :as fs-lib]
[clojure.data.json :as json]
[clojure.tools.logging :as log]))

(defn add-env-to-path
[plugin-env-dir]
(let [env-bin-path (fs-lib/join-paths plugin-env-dir "bin")
path (get-path-variable)]
(str env-bin-path ":" path)))

(defn make-args-json!
"Render arguments json file."
[template-file context output-file]
(log/info (format "Render Template (%s) with Environment Context: %s" template-file context))
(let [template (slurp template-file)
args-json (parser/render template context)]
(spit output-file (json/write-str args-json))))

(defn call-corrplot!
[input-file output-file plugin-env-dir]
(shell/with-sh-env {:PATH (add-env-to-path plugin-env-dir)
:R_PROFILE_USER (fs-lib/join-paths plugin-env-dir "Rprofile")
:LC_ALL "en_US.utf-8"
:LANG "en_US.utf-8"}
(let [command ["bash" "-c" (format "corrplot.sh -i %s -o %s" input-file output-file)]
result (apply sh command)
status (if (= (:exit result) 0) "Success" "Error")
msg (str (:out result) "\n" (:err result))]
{:status status
:msg msg})))

+ 7
- 0
test/tservice/plugins/corrplot_test.clj Näytä tiedosto

@@ -0,0 +1,7 @@
(ns tservice.plugins.corrplot-test
(:require [clojure.test :refer :all]
[tservice.plugins.corrplot :refer :all]))

(deftest a-test
(testing "FIXME, I fail."
(is (= 0 1))))

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