Use Artifacts.toml to access VARNA jar file (#12)

* Use Artifacts.toml to access VARNA jar file

* Have to use LazyArtifacts for a lazy artifact

* Improve README for java and artifacts instructions

Author: marcom

Artifacts.toml

@@ -0,0 +1,7 @@
+[VARNAv3-93_jar]
+git-tree-sha1 = "7141dcd09e8fced75b19ca928bd4a790af61ffc2"
+lazy = true
+
+    [[VARNAv3-93_jar.download]]
+    sha256 = "58e19c60214ca15f8aefe91ba0feafde3c21b2f30700d8b5b718a3c5bf7aaa5d"
+    url = "https://gist.github.com/marcom/e9f305a65fc6fbd0fef6df2d66d92f88/raw/7141dcd09e8fced75b19ca928bd4a790af61ffc2.tar.gz"

Project.toml

@@ -6,11 +6,11 @@ version = "0.3.0"
 [deps]
 BioStockholm = "eeb925a3-6f9d-43e6-829e-e0ea03b76ecf"
 ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
+LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 R2R_jll = "1e27f72a-4876-5c10-8678-3341fdb8ba55"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
-Scratch = "6c6a2e73-6563-6170-7368-637461726353"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 ViennaRNA = "05a721ad-238d-4945-8c85-8b5c1fff3465"
 
@@ -31,7 +31,6 @@ Luxor = "3.3"
 PrecompileTools = "1"
 R2R_jll = "=1.0.6"
 Requires = "1.3"
-Scratch = "1.1"
 UnicodePlots = "3"
 ViennaRNA = "0.11"
 julia = "1.6"

README.md

@@ -109,14 +109,14 @@ VARNA.plot_compare(dbn1="(((.....)))", seq1="GCGAAAAACGC",
 You will need a working Java installation (can be headless i think).
 You can test this by running:
 ```julia
-run(`java -version`)
+Sys.which("java")
 ```
-If you don't get an error, plotting with VARNA should work.
+If you get a file path (e.g. `"/usr/bin/java"`) and not `nothing`,
+plotting with VARNA should work.
 
 The VARNA jar file will get downloaded automatically the first time
-you plot something with VARNA. It gets stored in a scratch space that
-gets cleaned up by the Julia package manager when you uninstall
-PlotRNA.
+you plot something with one of the VARNA functions. It gets stored in
+the Julia artifacts directory.
 
 
 #### VARNA plot options

src/varna.jl

@@ -5,25 +5,9 @@ module VARNA
 #   `-foo` : error, no argument for option foo
 #   `-foo bar` : no error or warning
 
-using Scratch: @get_scratch!
-
-const _download_url = "https://varna.lri.fr/bin/VARNAv3-93.jar"
-
-# this will be filled in by `__init__()`
-_download_cache = ""
-
-function __init__()
-    global _download_cache = @get_scratch!("jar")
-end
-
-function _download_varna_jar(url=_download_url)
-    fname = joinpath(_download_cache, basename(url))
-    if !isfile(fname)
-        @info "downloading VARNA jar file from $url"
-        download(url, fname)
-    end
-    return fname
-end
+# TODO, this doesn't work: using LazyArtifacts: @artifact_str
+using LazyArtifacts
+_get_varna_jar() = artifact"VARNAv3-93_jar/VARNAv3-93.jar"
 
 # VARNA-3.93 supported formats: JPEG,PNG,EPS,XFIG,SVG
 const _map_fileendings_to_mime = Dict(
@@ -187,7 +171,7 @@ function plot(dbn::AbstractString;
               fileformat::AbstractString="svg",
               verbose::Bool=false,
               plot_opts...)
-    varna_jarpath = _download_varna_jar()
+    varna_jarpath = _get_varna_jar()
     if length(dbn) != length(seq)
         throw(ArgumentError("structure and sequence must have same length: $(length(dbn)) != $(length(seq))"))
     end
@@ -226,7 +210,7 @@ function plot_compare(; dbn1::AbstractString,
                       fileformat::AbstractString="svg",
                       verbose::Bool=false,
                       plot_opts...)
-    varna_jarpath = _download_varna_jar()
+    varna_jarpath = _get_varna_jar()
     if length(dbn1) != length(dbn2) || length(dbn1) != length(seq1) || length(dbn1) != length(seq2)
         throw(ArgumentError("all structures and sequences must have same length, here they are: " *
             "dbn1=$(length(dbn1)), seq1=$(length(seq1)), dbn2=$(length(dbn2)), seq2=$(length(seq2)))"))