From 01a235fd8802b94b7834a65baed970f5dbb77fff Mon Sep 17 00:00:00 2001
From: = <matti.pastell@helsinki.fi>
Date: Sat, 23 Apr 2016 19:18:44 +0300
Subject: [PATCH] Fix to deserialing cached content. Caching now works as
 previously documented and tests pass

---
 REQUIRE          |  2 +-
 src/cache.jl     | 25 +++++--------------------
 src/run.jl       | 15 ++++++++++-----
 test/runtests.jl |  5 ++---
 4 files changed, 18 insertions(+), 29 deletions(-)

diff --git a/REQUIRE b/REQUIRE
index c432c42..e50c478 100644
--- a/REQUIRE
+++ b/REQUIRE
@@ -1,4 +1,4 @@
 julia 0.4
 Compat
 ArgParse
-JSON
+JLD
diff --git a/src/cache.jl b/src/cache.jl
index 1de1dc5..2476f11 100644
--- a/src/cache.jl
+++ b/src/cache.jl
@@ -1,49 +1,34 @@
-import JSON, JLD
+import JLD
 
 function write_cache(doc::WeaveDoc, cache_path)
     cache_dir = "$(doc.cwd)/$cache_path"
     isdir(cache_dir) || mkpath(cache_dir)
-    name = "$cache_dir/$(doc.basename).json"
     JLD.save("$cache_dir/$(doc.basename).jld", Dict("doc" => doc))
-    open(name, "w") do io
-        write(io, JSON.json(doc))
-    end
     return nothing
 end
 
 function read_cache(doc::WeaveDoc, cache_path)
-    #name = "$(doc.cwd)/$cache_path/$(doc.basename).json"
     name = "$(doc.cwd)/$cache_path/$(doc.basename).jld"
     isfile(name) || return nothing
-    #parsed = JSON.parsefile(name)
     return JLD.load(name)["doc"]
 end
 
-#read_cache returns a dictionary, parse to back to chunk
+
 function restore_chunk(chunk::CodeChunk, cached)
     chunks = filter(x -> x.number == chunk.number &&
             string(typeof(x)) == "Weave.CodeChunk", cached.chunks)
 
-    #Chunk types, don't match after loading. Need to reinitialize
+    #Chunk types, don't match after loading. Fix by constructing chunks
+    #from loaded content
     new_chunks = Any[]
     for c in chunks
       newc = CodeChunk(c.content, c.number, c.start_line, c.optionstring, c.options)
       newc.result_no = c.result_no
       newc.figures = c.figures
       newc.result = c.result
+      newc.output = c.output
       push!(new_chunks, newc)
     end
-    #options = Dict{Symbol, Any}()
-    #info(cached["chunks"][idx])
-    #for (keys,vals) = cached["chunks"][idx]["options"]
-    #    options[symbol(keys)] = vals
-    #end
-    #haskey(options, :term_state) && (options[:term_state] = symbol(options[:term_state]))
-    #chunk.options = options
-    #chunk.content = cached["chunks"][idx]["content"]
-    #chunk.output = cached["chunks"][idx]["output"]
-    #chunk.figures = cached["chunks"][idx]["figures"]
-
     return new_chunks
 end
 
diff --git a/src/run.jl b/src/run.jl
index cc82ebb..6be773e 100644
--- a/src/run.jl
+++ b/src/run.jl
@@ -53,7 +53,15 @@ function Base.run(doc::WeaveDoc; doctype = :auto, plotlib="Gadfly",
 
     for i = 1:n
         chunk = doc.chunks[i]
-        if cached != nothing && (cache == :all || (cache ==:user && chunk.options[:cache]))
+
+        if typeof(chunk) == CodeChunk
+            options = merge(rcParams[:chunk_defaults], chunk.options)
+            merge!(chunk.options, options)
+        end
+
+        restore = (cache ==:user && typeof(chunk) == CodeChunk && chunk.options[:cache])
+
+        if cached != nothing && (cache == :all || restore)
             result_chunks = restore_chunk(chunk, cached)
         else
             result_chunks = run_chunk(chunk, report, SandBox)
@@ -89,9 +97,6 @@ end
 
 
 function run_chunk(chunk::CodeChunk, report::Report, SandBox::Module)
-    #Defaults, already merged before, this merges format specific things
-    options = merge(rcParams[:chunk_defaults], chunk.options)
-    merge!(chunk.options, options)
     result_chunk = eval_chunk(chunk, report, SandBox)
 end
 
@@ -293,7 +298,7 @@ function collect_results(chunk::CodeChunk, fmt::ScriptResult)
     end
     if content != ""
         startswith(content, "\n") || (content = "\n" * content)
-        rchunk = CodeChunk(content, chunk.number, chunk.start_line, chunk.option_AbstractString, copy(chunk.options))
+        rchunk = CodeChunk(content, chunk.number, chunk.start_line, chunk.optionstring, copy(chunk.options))
         push!(result_chunks, rchunk)
     end
 
diff --git a/test/runtests.jl b/test/runtests.jl
index 4e7c945..e43caa6 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -9,9 +9,8 @@ using Base.Test
 info("Test: Chunk options")
 include("chunk_options.jl")
 
-# Cache is currently not implemented for new output format
-#info("Test: Caching")
-#include("cache_test.jl")
+info("Test: Caching")
+include("cache_test.jl")
 
 if VERSION < v"0.5-dev"
   info("Test: Chunk options with Gadfly")