Add citation parser for markdown

src/WeaveMarkdown/markdown.jl

@@ -2,11 +2,24 @@
 module WeaveMarkdown
 using Markdown
 import Markdown: @trigger, @breaking, Code, MD, withstream, startswith, LaTeX
+using BibTeX
 
 mutable struct Comment
     text::String
 end
 
+mutable struct Citation
+    key::String
+    no::Int64
+    bib::Dict
+end
+
+Citation(key, no) = Citation(key, no, Dict())
+
+mutable struct Citations
+    content::Array{Citation}
+end
+
 @breaking true ->
 function dollarmath(stream::IO, block::MD)
     withstream(stream) do
@@ -61,8 +74,45 @@ function comment(stream::IO, md::MD)
     end
 end
 
+global const CITATIONS = Dict{Symbol, Any}(
+    :no => 1,
+    :bibtex => Dict(),
+    :references => []
+    )
+
+@trigger '[' ->
+function citation(stream::IO, md::MD)
+    withstream(stream) do
+        Markdown.startswith(stream, "[@") || return
+        text = Markdown.readuntil(stream, ']', match = '[')
+        text ≡ nothing && return
+        citations = strip.(split(text, ";"))
+        cites = Citation[]
+        for c in citations
+            c = replace(c, r"^@" => "")
+            #Check for matcthing bixtex key
+            if haskey(CITATIONS[:bibtex], c)
+                bib = CITATIONS[:bibtex][c]
+                # Check for repeated citations
+                if haskey(CITATIONS[:refnumbers], c)
+                    no = CITATIONS[:refnumbers][c]
+                else
+                    no = CITATIONS[:no]
+                    CITATIONS[:refnumbers][c] = no
+                    CITATIONS[:no] += 1
+                end
+                push!(cites, Citation(c, no, bib))
+                CITATIONS[:references][c] = bib
+            else
+                push!(cites, Citation(c, 0))
+            end
+        end
+        return Citations(cites)
+    end
+end
+
 # Create own flavor and copy all the features from julia flavor
-Markdown.@flavor weavemd [dollarmath, comment, topcomment]
+Markdown.@flavor weavemd [dollarmath, comment, topcomment, citation]
 weavemd.breaking = [weavemd.breaking; Markdown.julia.breaking]
 weavemd.regular = [weavemd.regular; Markdown.julia.regular]
 for key in keys(Markdown.julia.inner)
@@ -73,6 +123,17 @@ for key in keys(Markdown.julia.inner)
     end
 end
 
+function parse_markdown(text, bibfile)
+    CITATIONS[:no] = 1
+    header, refs = parse_bibtex(read(bibfile, String))
+    CITATIONS[:bibtex] = refs
+    CITATIONS[:references] = Dict()
+    CITATIONS[:refnumbers] = Dict()
+    m = Markdown.parse(text, flavor = weavemd);
+    m.content
+end
+
+
 include("html.jl")
 include("latex.jl")
 end

test/documents/bibtex/testdocs.bib

@@ -0,0 +1,41 @@
+
+@Article{LubiDunn15,
+  Title                    = {Computing in Operations Research Using Julia},
+  Author                   = {Miles Lubin and Iain Dunning},
+  Journal                  = {INFORMS Journal on Computing},
+  Year                     = {2015},
+  Number                   = {2},
+  Pages                    = {238--248},
+  Volume                   = {27},
+  Optdoi                   = {10.1287/ijoc.2014.0623},
+  Opturl                   = {http://dx.doi.org/10.1287/ijoc.2014.0623}
+}
+
+@article{pastell_filtering_2018,
+	title = {Filtering methods to improve the accuracy of indoor positioning data for dairy cows},
+	volume = {169},
+	issn = {1537-5110},
+	url = {http://www.sciencedirect.com/science/article/pii/S1537511017308711},
+	doi = {10.1016/j.biosystemseng.2018.01.008},
+	urldate = {2018-03-28},
+	journal = {Biosystems Engineering},
+	author = {Pastell, Matti and Frondelius, Lilli and Järvinen, Mikko and Backman, Juha},
+	month = may,
+	year = {2018},
+	keywords = {Indoor positioning, Dairy, Extended Kalman filter, Ultra-wide band},
+	pages = {22--31}
+}
+
+@article{Bezanson2017,
+  doi = {10.1137/141000671},
+  url = {https://doi.org/10.1137/141000671},
+  year  = {2017},
+  month = {jan},
+  publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
+  volume = {59},
+  number = {1},
+  pages = {65--98},
+  author = {Jeff Bezanson and Alan Edelman and Stefan Karpinski and Viral B. Shah},
+  title = {Julia: A Fresh Approach to Numerical Computing},
+  journal = {{SIAM} Review}
+}

test/markdown_test.jl

@@ -100,3 +100,20 @@ Multiple lines
 
 @test WeaveMarkdown.html(md.content[2]) == "<p class=\"math\">\\[\nx = 2\n\\]</p>"
 @test WeaveMarkdown.html(md.content[4]) == "\n<!-- \nMultiple lines\n  -->\n"
+
+##
+using Revise
+import Weave: WeaveMarkdown
+
+md = """
+
+[@Bezanson2017]
+
+citing [@pastell_filtering_2018; @someref]
+
+cite [@Bezanson2017] again
+
+"""
+
+m = WeaveMarkdown.parse_markdown(md, "test/documents/bibtex/testdocs.bib");
+m