Added error handling with html display (#117)

* Implemented error handling and initial html display

* Improved html display and tests for error handling

Author: mpastell

src/Weave.jl

@@ -68,6 +68,8 @@ Weave an input document to output file.
 * `cache_path`: where of cached output will be saved.
 * `cache`: controls caching of code: `:off` = no caching, `:all` = cache everything,
   `:user` = cache based on chunk options, `:refresh`, run all code chunks and save new cache.
+* `throw_errors` if `false` errors are included in output document and the whole document is 
+    executed. if `true` errors are thrown when they occur.
 * `template` : Template (file path) for md2html or md2tex formats.
 * `highlight_theme` : Theme (Highlights.AbstractTheme) for used syntax highlighting
 * `css` : CSS (file path) used for md2html format
@@ -79,6 +81,7 @@ function weave(source ; doctype = :auto, plotlib=:auto,
         informat=:auto, out_path=:doc, args = Dict(),
         fig_path = "figures", fig_ext = nothing,
         cache_path = "cache", cache=:off,
+        throw_errors = false,
         template = nothing, highlight_theme = nothing, css = nothing,
         latex_cmd = "xelatex")
 
@@ -91,7 +94,8 @@ function weave(source ; doctype = :auto, plotlib=:auto,
     try
       doc = run(doc, doctype = doctype, plotlib=plotlib,
               out_path=out_path, args = args,
-              fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path, cache=cache)
+              fig_path = fig_path, fig_ext = fig_ext, cache_path = cache_path, cache=cache,
+              throw_errors = throw_errors)
       formatted = format(doc)
 
       outname = get_outname(out_path, doc)

src/display_methods.jl

@@ -15,10 +15,12 @@ mutable struct Report <: Display
   mimetypes::Array{AbstractString}
   first_plot::Bool
   header_script::String
+  throw_errors::Bool
 end
 
-function Report(cwd, basename, formatdict, mimetypes)
-    Report(cwd, basename, formatdict, "", "", "", 1, AbstractString[], :text, nothing, mimetypes, true, "")
+function Report(cwd, basename, formatdict, mimetypes, throw_errors)
+    Report(cwd, basename, formatdict, "", "", "", 1, AbstractString[], :text, nothing,
+        mimetypes, true, "", throw_errors)
 end
 
 
@@ -34,13 +36,14 @@ function Base.display(report::Report, data)
         if mimewritable(m, data)
             try
                 if !istextmime(m)
-                    Compat.invokelatest(display, report, m, data)   
+                    Compat.invokelatest(display, report, m, data)
                 elseif report.cur_chunk.options[:term]
                     Compat.invokelatest(display, report, "text/plain", data)
-                else   
+                else
                     Compat.invokelatest(display, report, m, data)
                 end
             catch e
+                throw(e)
                 warn("Failed to display data in \"$m\" format")
                 continue
             end
@@ -71,6 +74,20 @@ function Base.display(report::Report, m::MIME"text/plain", data)
     println(s)
 end
 
+function Base.display(report::Report, m::MIME"text/plain", data::Exception)
+    println("Error: " * sprint(showerror, data))
+end
+
+function Base.display(report::Report, m::MIME"text/html", data::Exception)
+    report.rich_output = sprint(show, m, data)
+end
+
+function Base.show(io, m::MIME"text/html", data::Exception)
+    println(io ,"<pre class=\"julia-error\">")
+    println(io, Base.Markdown.htmlesc("ERROR: " * sprint(showerror, data)))
+    println(io ,"</pre>")
+end
+
 #Catch "rich_output"
 function Base.display(report::Report, m::MIME"text/html", data)
     s = reprmime(m, data)
@@ -88,7 +105,6 @@ function Base.display(report::Report, m::MIME"text/latex", data)
     report.rich_output *= "\n" * s
 end
 
-
 """Add saved figure name to results and return the name"""
 function add_figure(report::Report, data, m, ext)
   chunk = report.cur_chunk

src/run.jl

@@ -22,7 +22,7 @@ Run code chunks and capture output from parsed document.
 """
 function Base.run(doc::WeaveDoc; doctype = :auto, plotlib=:auto,
         out_path=:doc, args=Dict(), fig_path = "figures", fig_ext = nothing,
-        cache_path = "cache", cache = :off)
+        cache_path = "cache", cache = :off, throw_errors=false)
     #cache :all, :user, :off, :refresh
 
     doc.cwd = get_cwd(doc, out_path)
@@ -60,7 +60,7 @@ function Base.run(doc::WeaveDoc; doctype = :auto, plotlib=:auto,
     rcParams[:plotlib_set] = false
     plotlib == :auto || init_plotting(plotlib)
 
-    report = Report(doc.cwd, doc.basename, doc.format.formatdict, mimetypes)
+    report = Report(doc.cwd, doc.basename, doc.format.formatdict, mimetypes, throw_errors)
     pushdisplay(report)
 
     if cache != :off && cache != :refresh
@@ -204,7 +204,7 @@ function run_code(chunk::CodeChunk, report::Report, SandBox::Module)
         lastline = (result_no == N)
         rcParams[:plotlib_set] || detect_plotlib(chunk) #Try to autodetect plotting library
         (obj, out) = capture_output(expr, SandBox, chunk.options[:term],
-                      chunk.options[:display], rcParams[:plotlib], lastline)
+                      chunk.options[:display], rcParams[:plotlib], lastline, report.throw_errors)
         figures = report.figures #Captured figures
         result = ChunkOutput(str_expr, out, report.cur_result, report.rich_output, figures)
         report.rich_output = ""
@@ -223,7 +223,7 @@ end
 getstdout() = Base.STDOUT
 
 function capture_output(expr, SandBox::Module, term, disp, plotlib,
-                        lastline)
+                        lastline, throw_errors=false)
     #oldSTDOUT = STDOUT
     oldSTDOUT = getstdout()
     out = nothing
@@ -243,6 +243,10 @@ function capture_output(expr, SandBox::Module, term, disp, plotlib,
         elseif lastline && obj != nothing
             (expr.head != :toplevel && expr.head != :(=)) && display(obj)
         end
+    catch E
+        throw_errors && throw(E)
+        display(E)
+        warn("ERROR: $(typeof(E)) occurred, including output in Weaved document")    
     finally
         redirect_stdout(oldSTDOUT)
         close(wr)

templates/pandoc_skeleton.css

@@ -518,6 +518,10 @@ pre.sourceCode.julia {
   border-radius: 4px;
 }
 
+pre.julia-error {
+  color : red
+}
+
 code,
 kbd,
 pre,

templates/skeleton_css.css

@@ -515,6 +515,10 @@ pre.sourceCode.julia {
   border-radius: 4px;
 }
 
+pre.julia-error {
+  color : red
+}
+
 code,
 kbd,
 pre,

test/errors_test.jl

@@ -0,0 +1,43 @@
+using Weave
+using Base.Test
+
+s1= """
+
+```julia
+using NonExisting
+```
+
+```julia
+x =
+```
+
+
+```julia;term=true
+plot(x)
+y = 10
+print(y
+```
+
+"""
+
+p1 = Weave.parse_doc(s1, "markdown")
+doc = Weave.WeaveDoc("dummy1.jmd", p1, Dict())
+doc1 = Weave.run(doc, doctype = "pandoc")
+
+@test doc1.chunks[1].output == "Error: ArgumentError: Module NonExisting not found in current path.\nRun `Pkg.add(\"NonExisting\")` to install the NonExisting package.\n"
+@test doc1.chunks[2].output == "Error: syntax: incomplete: premature end of input\n"
+@test doc1.chunks[3].output == "\njulia> plot(x)\nError: UndefVarError: plot not defined\n\njulia> y = 10\n10\n\njulia> print(y\nError: syntax: incomplete: premature end of input\n"
+
+try
+    doc2 = Weave.run(doc, doctype = "pandoc", throw_errors = true)
+catch E
+    @test typeof(E) == ArgumentError
+    @test E.msg == "Module NonExisting not found in current path.\nRun `Pkg.add(\"NonExisting\")` to install the NonExisting package."
+end
+
+doc = Weave.WeaveDoc("dummy1.jmd", p1, Dict())
+doc3 = Weave.run(doc, doctype = "md2html")
+@test doc3.chunks[1].rich_output == "<pre class=\"julia-error\">\nERROR: ArgumentError: Module NonExisting not found in current path.\nRun &#96;Pkg.add&#40;&quot;NonExisting&quot;&#41;&#96; to install the NonExisting package.\n</pre>\n"
+@test doc3.chunks[2].rich_output == "<pre class=\"julia-error\">\nERROR: syntax: incomplete: premature end of input\n</pre>\n"
+@test doc3.chunks[3].output == "\njulia> plot(x)\nError: UndefVarError: plot not defined\n\njulia> y = 10\n10\n\njulia> print(y\nError: syntax: incomplete: premature end of input\n"
+@test doc3.chunks[3].rich_output == ""

test/runtests.jl

@@ -4,6 +4,9 @@ using Base.Test
 info("Test: Chunk options")
 include("chunk_options.jl")
 
+info("Testing error handling")
+include("errors_test.jl")
+
 info("Test: Converting")
 include("convert_test.jl")
 
@@ -32,4 +35,3 @@ include("chunk_opts_gadfly.jl")
 info("Test: Weaving with Plots.jl")
 include("plotsjl_test.jl")
 include("publish_test.jl")
-