tservice-plugins
/
quartet-metqc-report
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First Commit.

tags/v0.1.0
YJC pirms 3 gadiem
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  1. +11
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      .gitignore
  2. +277
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      LICENSE.md
  3. +42
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      README.md
  4. +29
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      project.clj
  5. +1
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      resources/.Rprofile
  6. +1
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      resources/general-information.json
  7. +114
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      resources/quartet-metqc-report/bin/metqc.sh
  8. +711
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      resources/renv.lock
  9. +5
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      resources/renv/.gitignore
  10. +653
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      resources/renv/activate.R
  11. +7
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      resources/renv/settings.dcf
  12. +1
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      resources/requirements.txt
  13. +28
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      resources/tservice-plugin.yaml
  14. +143
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      src/tservice/plugins/quartet_metqc_report.clj
  15. +54
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      src/tservice/plugins/quartet_metqc_report/metqc.clj

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

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LICENSE.md Parādīt failu

Eclipse Public License - v 2.0

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+ 42
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README.md Parādīt failu

# quartet-metqc-report

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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project.clj Parādīt failu

(defproject tservice/quartet-metqc-report "v0.1.0"
:description "Visualizes Quality Control(QC) results for Quartet Project."
:url "https://github.com/tservice-plugins/quartet-metqc-report"
: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/data.csv "1.0.0"]
[me.raynes/fs "1.4.6"]
[org.clojure/tools.logging "1.1.0"]
[org.clojure/core.async "0.4.500"
:exclusions [org.clojure/tools.reader]]]

:profiles
{:provided
{:dependencies
[[org.clojure/clojure "1.10.1"]
[org.clojars.yjcyxky/tservice "0.5.8"]]}

: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 "quartet-metqc-report.tservice-plugin.jar"}})

+ 1
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resources/.Rprofile Parādīt failu

source("renv/activate.R")

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resources/general-information.json Parādīt failu

{}

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resources/quartet-metqc-report/bin/metqc.sh Parādīt failu

#!/usr/bin/env bash

# A wrapper for metqc r package
#
# 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 <DATA_FILE>] [-m <META_FILE>] [-o <RESULT_DIR>]
-d DATA_FILE Proteomics profiled data.
-m META_FILE Metadata file.
-o RESULT_DIR A directory for result files.
EOF
}

while getopts ":hd:m:o:" arg; do
case "$arg" in
"d")
DATA_FILE="$OPTARG"
;;
"m")
META_FILE="$OPTARG"
;;
"o")
RESULT_DIR="$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 "$DATA_FILE" ]; then
echo "-d argument is not specified."
exit 1
elif [ ! -f "$DATA_FILE" ]; then
echo "$DATA_FILE is not a valid file."
exit 1
else
DATA_FILE=$(realpath $DATA_FILE)
fi

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

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

TEMP=$(mktemp)

echo "Run script: $TEMP"

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

run <- function() {
# Print traceback message
on.exit(traceback())
library(MetQC)
print("Running...")
MetQC::GetPerformance(dt.path="$DATA_FILE", metadata.path="$META_FILE", output.path="$RESULT_DIR")
MetQC::CountSNR(dt.path="$DATA_FILE", metadata.path="$META_FILE", output.path="$RESULT_DIR")
MetQC::CountCTR(dt.path="$DATA_FILE", metadata.path="$META_FILE", output.path="$RESULT_DIR")
}

run()
EOF

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

Rscript $TEMP

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resources/renv.lock Parādīt failu

{
"R": {
"Version": "3.6.3",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://cloud.r-project.org"
}
]
},
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"Version": "2.23-16",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "997471f25a7ed6c782f0090ce52cc63a"
},
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"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"
},
"MetQC": {
"Package": "MetQC",
"Version": "0.3.5",
"Source": "GitHub",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteRepo": "MetQC",
"RemoteUsername": "chinese-quartet",
"RemoteRef": "v0.3.5",
"RemoteSha": "73c0f17fee22985a16ca6d670ddeb4b2af462fd7",
"Hash": "7f59a7bebf21b695a35f212db3f23f9a"
},
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"Repository": "CRAN",
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"Repository": "CRAN",
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"Repository": "CRAN",
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"Repository": "CRAN",
"Hash": "e3ae5d68dea0c55a12ea12a9fda02e61"
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"Repository": "CRAN",
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"Package": "fastmap",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "77bd60a6157420d4ffa93b27cf6a58b8"
},
"foreign": {
"Package": "foreign",
"Version": "0.8-75",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9a7efaa7320b9f327a904d1e615b0b46"
},
"fs": {
"Package": "fs",
"Version": "1.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "44594a07a42e5f91fac9f93fda6d0109"
},
"gert": {
"Package": "gert",
"Version": "1.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "72b34cde959b806e86cb99fc12d1ba58"
},
"ggplot2": {
"Package": "ggplot2",
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"Repository": "CRAN",
"Hash": "d7566c471c7b17e095dd023b9ef155ad"
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"Package": "gh",
"Version": "1.3.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "38c2580abbda249bd6afeec00d14f531"
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"gitcreds": {
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"Repository": "CRAN",
"Hash": "f3aefccc1cc50de6338146b62f115de8"
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"Repository": "CRAN",
"Hash": "6efd734b14c6471cfe443345f3e35e29"
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"Repository": "CRAN",
"Hash": "ac5c6baf7822ce8732b343f14c072c4d"
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"Repository": "CRAN",
"Hash": "8eb36c8125038e648e5d111c0d7b2ed4"
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"Source": "Repository",
"Repository": "CRAN",
"Hash": "a525aba14184fec243f9eaec62fbed43"
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"ini": {
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"Version": "0.3.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6154ec2223172bce8162d4153cda21f7"
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"Version": "0.2.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7ab57a6de7f48a8dc84910d1eca42883"
},
"jsonlite": {
"Package": "jsonlite",
"Version": "1.7.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "98138e0994d41508c7a6b84a0600cfcb"
},
"knitr": {
"Package": "knitr",
"Version": "1.34",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "aa958054ac6f0360926bb952ea302f0f"
},
"labeling": {
"Package": "labeling",
"Version": "0.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "3d5108641f47470611a32d0bdf357a72"
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"lattice": {
"Package": "lattice",
"Version": "0.20-38",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "848f8c593fd1050371042d18d152e3d7"
},
"lifecycle": {
"Package": "lifecycle",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "3471fb65971f1a7b2d4ae7848cf2db8d"
},
"magrittr": {
"Package": "magrittr",
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"Source": "Repository",
"Repository": "CRAN",
"Hash": "41287f1ac7d28a92f0a286ed507928d3"
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"memoise": {
"Package": "memoise",
"Version": "2.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a0bc51650201a56d00a4798523cc91b3"
},
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"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"
},
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"Package": "nlme",
"Version": "3.1-144",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e80d41932d3cc235ccbbbb9732ae162e"
},
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"Package": "nnet",
"Version": "7.3-12",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "68287aec1f476c41d16ce1ace445800c"
},
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"Repository": "CRAN",
"Hash": "5406fd37ef0bf9b88c8a4f264d6ec220"
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"Repository": "CRAN",
"Hash": "43f228eb4b49093d1c8a5c93cae9efe9"
},
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"Package": "pkgbuild",
"Version": "1.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "725fcc30222d4d11ec68efb8ff11a9af"
},
"pkgconfig": {
"Package": "pkgconfig",
"Version": "2.0.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "01f28d4278f15c76cddbea05899c5d6f"
},
"pkgload": {
"Package": "pkgload",
"Version": "1.2.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "53139eedf68b98eecd5289664969c3f2"
},
"praise": {
"Package": "praise",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a555924add98c99d2f411e37e7d25e9f"
},
"prettyunits": {
"Package": "prettyunits",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "95ef9167b75dde9d2ccc3c7528393e7e"
},
"processx": {
"Package": "processx",
"Version": "3.5.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0cbca2bc4d16525d009c4dbba156b37c"
},
"ps": {
"Package": "ps",
"Version": "1.6.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "32620e2001c1dce1af49c49dccbb9420"
},
"purrr": {
"Package": "purrr",
"Version": "0.3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "97def703420c8ab10d8f0e6c72101e02"
},
"rappdirs": {
"Package": "rappdirs",
"Version": "0.3.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5e3c5dc0b071b21fa128676560dbe94d"
},
"rcmdcheck": {
"Package": "rcmdcheck",
"Version": "1.3.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ed95895886dab6d2a584da45503555da"
},
"rematch2": {
"Package": "rematch2",
"Version": "2.1.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "76c9e04c712a05848ae7a23d2f170a40"
},
"remotes": {
"Package": "remotes",
"Version": "2.4.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a85ebb35721573b196317b49ddd2dfe4"
},
"renv": {
"Package": "renv",
"Version": "0.13.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9f10d9db5b50400c348920c5c603385e"
},
"rlang": {
"Package": "rlang",
"Version": "0.4.11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "515f341d3affe0de9e4a7f762efb0456"
},
"roxygen2": {
"Package": "roxygen2",
"Version": "7.1.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "eb9849556c4250305106e82edae35b72"
},
"rpart": {
"Package": "rpart",
"Version": "4.1-15",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9787c1fcb680e655d062e7611cadf78e"
},
"rprojroot": {
"Package": "rprojroot",
"Version": "2.0.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "249d8cd1e74a8f6a26194a91b47f21d1"
},
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"Package": "rstudioapi",
"Version": "0.13",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "06c85365a03fdaf699966cc1d3cf53ea"
},
"rversions": {
"Package": "rversions",
"Version": "2.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f88fab00907b312f8b23ec13e2d437cb"
},
"scales": {
"Package": "scales",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6f76f71042411426ec8df6c54f34e6dd"
},
"sessioninfo": {
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"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "308013098befe37484df72c39cf90d6e"
},
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"Package": "spatial",
"Version": "7.3-11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f27a078d834614513608da2c08031130"
},
"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"
},
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"Version": "3.1-8",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ad25122f95d04988f6f79d69aaadd53d"
},
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"Version": "3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b227d13e29222b4574486cfcbde077fa"
},
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"Package": "testthat",
"Version": "3.0.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "575216c9946ca70016c3ffb9c31709ba"
},
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"Hash": "360e904f9e623286e1a0c6ca0a98c5f6"
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"Repository": "CRAN",
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"Repository": "CRAN",
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},
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"Package": "viridisLite",
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"Repository": "CRAN",
"Hash": "55e157e2aa88161bdb0754218470d204"
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"Repository": "CRAN",
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"xml2": {
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"Repository": "CRAN",
"Hash": "d4d71a75dd3ea9eb5fa28cc21f9585e2"
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"Repository": "CRAN",
"Hash": "6c85f015dee9cc7710ddd20f86881f58"
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"Version": "2.2.1",
"Source": "Repository",
"Repository": "CRAN",
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"zip": {
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"Hash": "c7eef2996ac270a18c2715c997a727c5"
}
}
}

+ 5
- 0
resources/renv/.gitignore Parādīt failu

library/
local/
lock/
python/
staging/

+ 653
- 0
resources/renv/activate.R Parādīt failu


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 Parādīt failu

external.libraries:
ignored.packages:
package.dependency.fields: Imports, Depends, LinkingTo
r.version:
snapshot.type: all
use.cache: TRUE
vcs.ignore.library: TRUE

+ 1
- 0
resources/requirements.txt Parādīt failu

git+git://github.com/chinese-quartet/quartet-metabolite-report@v1.0.0

+ 28
- 0
resources/tservice-plugin.yaml Parādīt failu

info:
name: QC Report for Quartet Metabolomics
version: v0.1.1
description: Generate the QC Report for Quartet Metabolomics data.
category: Report
home: https://github.com/tservice-plugins/quartet-metqc-report
source: PGx
short_name: quartet-metqc-report
icons:
- src: ""
type: image/png
sizes: 192x192
author: PGx
plugin:
name: quartet-metqc-report
display-name: QC Report for Quartet Metabolomics
lazy-load: false
init:
# Unpack environment file to the directory, repository/envs/quartet-metqc-report
- step: unpack-env
envname: quartet-metqc-report
postunpack: chmod a+x {{ENV_DEST_DIR}}/bin/metqc.sh
- step: load-namespace
namespace: tservice.plugins.quartet-metqc-report
- step: register-plugin
entrypoint: tservice.plugins.quartet-metqc-report/metadata
- step: init-event
entrypoint: tservice.plugins.quartet-metqc-report/events-init

+ 143
- 0
src/tservice/plugins/quartet_metqc_report.clj Parādīt failu

(ns tservice.plugins.quartet-metqc-report
(:require [clojure.data.json :as json]
[clojure.spec.alpha :as s]
[spec-tools.core :as st]
[clojure.tools.logging :as log]
[tservice.lib.files :as ff]
[tservice.api.config :refer [add-env-to-path]]
[tservice.lib.fs :as fs-lib]
[tservice.vendor.multiqc :as mq]
[tservice.plugins.quartet-metqc-report.metqc :as metqc]
[tservice.api.task :refer [make-events-init publish-event! make-plugin-metadata create-task! update-process!]]))

;;; ------------------------------------------------ Event Specs ------------------------------------------------
(s/def ::metadata_file
(st/spec
{:spec (s/and string? #(re-matches #"^[a-zA-Z0-9]+:\/\/(\/|\.\/)[a-zA-Z0-9_]+.*" %))
:type :string
:description "File path for metadata file, such as file:///xxx/xxx/metadata.csv"
:swagger/default nil
:reason "The filepath must be string."}))

(s/def ::data_file
(st/spec
{:spec (s/and string? #(re-matches #"^[a-zA-Z0-9]+:\/\/(\/|\.\/)[a-zA-Z0-9_]+.*" %))
:type :string
:description "File path for metabolomics profiled data, such as file:///xxx/xxx/data.csv"
:swagger/default nil
:reason "The filepath must be string."}))

(s/def ::name
(st/spec
{:spec string?
:type :string
:description "The name of the report"
:swagger/default ""
:reason "Not a valid name"}))

(s/def ::description
(st/spec
{:spec string?
:type :string
:description "Description of the report"
:swagger/default ""
:reason "Not a valid description."}))

(def quartet-metqc-report-params-body
"A spec for the body parameters."
(s/keys :req-un [::name ::data_file ::metadata_file]
:opt-un [::description]))

;;; ------------------------------------------------ Event Metadata ------------------------------------------------
(def metadata
(make-plugin-metadata
{:name "quartet-metqc-report"
:summary "Visualizes Quality Control(QC) results from metabolomics data for Quartet Project."
:params-schema quartet-metqc-report-params-body
:handler (fn [{:keys [name data_file metadata_file description]
:or {description (format "Quality control report for %s" name)}
:as payload}]
(let [payload (merge {:description description} payload)
data-file (metqc/correct-filepath data_file)
metadata-file (metqc/correct-filepath metadata_file)
workdir (metqc/dirname data-file)
log-path (fs-lib/join-paths workdir "log")
response {:report (format "%s/multiqc_report.html" workdir)
:log log-path
:response-type :data2report}
task-id (create-task! {:name name
:description description
:payload payload
:plugin-name "quartet-metqc-report"
:plugin-type "ReportPlugin"
:plugin-version "v0.1.0"
:response response})
result-dir (fs-lib/join-paths workdir "results")]
(fs-lib/create-directories! result-dir)
(log/info (format "Create a report %s with %s in %s" name payload workdir))
(spit log-path (json/write-str {:status "Running"
:msg ""}))
(update-process! task-id 0)
(publish-event! "quartet_metqc_report"
{:data-file data-file
:metadata-file metadata-file
:dest-dir workdir
:task-id task-id
:metadata {:name name
:description description
:plugin-name "quartet-metqc-report"
:plutin-type "ReportPlugin"
:plugin-version "v0.1.0"}})
response))
:plugin-type :ReportPlugin
:response-type :data2report}))

(defn update-log-process!
"Update message into log file and process into database."
[log-path coll task-id process]
(spit log-path (json/write-str coll))
(update-process! task-id process))

(defn date
[]
(.format (java.text.SimpleDateFormat. "yyyy-MM-dd")
(new java.util.Date)))

(defn- make-report!
[{:keys [data-file metadata-file dest-dir metadata task-id]}]
(let [log-path (fs-lib/join-paths dest-dir "log")
result-dir (fs-lib/join-paths dest-dir "results")
parameters-file (fs-lib/join-paths result-dir "general_information.json")
results (ff/chain-fn-coll [(fn []
(update-process! task-id 20)
(metqc/call-metqc! data-file metadata-file result-dir))
(fn []
(update-process! task-id 50)
(spit parameters-file (json/write-str {"Report Name" (:name metadata)
"Description" (:description metadata)
"Report Tool" (format "%s-%s"
(:plugin-name metadata)
(:plugin-version metadata))
"Team" "Quartet Team"
"Date" (date)}))
{:status "Success" :msg ""})
(fn []
(update-process! task-id 80)
(mq/multiqc result-dir dest-dir
{:template "quartet_metabolite_report"
:title "Quartet Report for Metabolomics"
:env {:PATH (add-env-to-path "quartet-metqc-report")}}))]
(fn [result] (= (:status result) "Success")))
status (:status (last results))
msg (apply str (map :msg results))
process (if (= status "Success") 100 -1)]
(log/info (format "Running batch command: %s" (pr-str results)))
(update-log-process! log-path {:status status
:msg msg}
task-id process)))

;;; --------------------------------------------------- Lifecycle ----------------------------------------------------

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

+ 54
- 0
src/tservice/plugins/quartet_metqc_report/metqc.clj Parādīt failu

(ns tservice.plugins.quartet-metqc-report.metqc
"A wrapper for metqc tool."
(:require [tservice.api.config :refer [add-env-to-path]]
[tservice.lib.files :refer [is-localpath? get-plugin-jar-env-dir]]
[clojure.string :as clj-str]
[tservice.lib.fs :as fs-lib]
[clojure.java.shell :as shell :refer [sh]]
[clojure.java.io :refer [file]]))

(defn call-metqc!
"Call metqc bash script. more details on https://github.com/chinese-quartet/MetQC
exp-file: Proteomics profiled data.
meta-file: proteomics metadata.
result-dir: A directory for result files.
"
[exp-file meta-file result-dir]
(shell/with-sh-env {:PATH (add-env-to-path "quartet-metqc-report")
:R_PROFILE_USER (fs-lib/join-paths (get-plugin-jar-env-dir "quartet-metqc-report") "Rprofile")
:LC_ALL "en_US.utf-8"
:LANG "en_US.utf-8"}
(let [command ["bash" "-c"
(format "metqc.sh -d %s -m %s -o %s" exp-file meta-file result-dir)]
result (apply sh command)
status (if (= (:exit result) 0) "Success" "Error")
msg (str (:out result) "\n" (:err result))]
{:status status
:msg msg})))

(defn correct-filepath
[filepath]
(if (is-localpath? filepath)
(clj-str/replace filepath #"^file:\/\/" "")
filepath))

(defn ^String basename
"Returns the basename of 'path'.
This works by calling getName() on a java.io.File instance. It's prefered
over last-dir-in-path for that reason.
Parameters:
path - String containing the path for an item in iRODS.
Returns:
String containing the basename of path."
[^String path]
(.getName (file path)))

(defn ^String dirname
"Returns the dirname of 'path'.
This works by calling getParent() on a java.io.File instance.
Parameters:
path - String containing the path for an item in iRODS.
Returns:
String containing the dirname of path."
[^String path]
(when path (.getParent (file path))))

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