Gexf

Manifest.toml

@@ -0,0 +1,218 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[ArnoldiMethod]]
+deps = ["DelimitedFiles", "LinearAlgebra", "Random", "SparseArrays", "StaticArrays", "Test"]
+git-tree-sha1 = "2b6845cea546604fb4dca4e31414a6a59d39ddcd"
+uuid = "ec485272-7323-5ecc-a04f-4719b315124d"
+version = "0.0.4"
+
+[[AutoHashEquals]]
+git-tree-sha1 = "45bb6705d93be619b81451bb2006b7ee5d4e4453"
+uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f"
+version = "0.2.0"
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[BinaryProvider]]
+deps = ["Libdl", "SHA"]
+git-tree-sha1 = "5b08ed6036d9d3f0ee6369410b830f8873d4024c"
+uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
+version = "0.5.8"
+
+[[CodecZlib]]
+deps = ["BinaryProvider", "Libdl", "TranscodingStreams"]
+git-tree-sha1 = "05916673a2627dd91b4969ff8ba6941bc85a960e"
+uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
+version = "0.6.0"
+
+[[DataStructures]]
+deps = ["InteractiveUtils", "OrderedCollections"]
+git-tree-sha1 = "b7720de347734f4716d1815b00ce5664ed6bbfd4"
+uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+version = "0.17.9"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[DelimitedFiles]]
+deps = ["Mmap"]
+uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[EzXML]]
+deps = ["Printf", "XML2_jll"]
+git-tree-sha1 = "0fa3b52a04a4e210aeb1626def9c90df3ae65268"
+uuid = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
+version = "1.1.0"
+
+[[FileIO]]
+deps = ["Pkg"]
+git-tree-sha1 = "2c84c57aced468fa21763c66d3bef33adcd09ec7"
+uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+version = "1.2.2"
+
+[[Inflate]]
+deps = ["Pkg", "Printf", "Random", "Test"]
+git-tree-sha1 = "b7ec91c153cf8bff9aff58b39497925d133ef7fd"
+uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9"
+version = "0.1.1"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[JLD2]]
+deps = ["CodecZlib", "DataStructures", "FileIO", "Mmap", "Pkg", "Printf", "UUIDs"]
+git-tree-sha1 = "5deae9f0745ef505ed155a0029629cf08502ccab"
+uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+version = "0.1.11"
+
+[[LibGit2]]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[Libiconv_jll]]
+deps = ["Libdl", "Pkg"]
+git-tree-sha1 = "802f5b23c846cb4ed568cae0bfb0ce0d2ba1926d"
+uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
+version = "1.16.0+1"
+
+[[LightGraphs]]
+deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
+git-tree-sha1 = "a0d4bcea4b9c056da143a5ded3c2b7f7740c2d41"
+uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
+version = "1.3.0"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[MacroTools]]
+deps = ["DataStructures", "Markdown", "Random"]
+git-tree-sha1 = "07ee65e03e28ca88bc9a338a3726ae0c3efaa94b"
+uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
+version = "0.5.4"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[MetaGraphs]]
+deps = ["JLD2", "LightGraphs", "Random"]
+git-tree-sha1 = "8900d368fa44bd61c7e598d6a0f577e347f3cf67"
+uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
+version = "0.6.5"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[Nullables]]
+git-tree-sha1 = "8f87854cc8f3685a60689d8edecaa29d2251979b"
+uuid = "4d1e1d77-625e-5b40-9113-a560ec7a8ecd"
+version = "1.0.0"
+
+[[OrderedCollections]]
+deps = ["Random", "Serialization", "Test"]
+git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1"
+uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+version = "1.1.0"
+
+[[ParserCombinator]]
+deps = ["AutoHashEquals", "Nullables", "Printf", "Test"]
+git-tree-sha1 = "370b7fcf9ee754bf47b86389caded06a140fffcc"
+uuid = "fae87a5f-d1ad-5cf0-8f61-c941e1580b46"
+version = "2.0.0"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Test", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[Requires]]
+deps = ["UUIDs"]
+git-tree-sha1 = "d37400976e98018ee840e0ca4f9d20baa231dc6b"
+uuid = "ae029012-a4dd-5104-9daa-d747884805df"
+version = "1.0.1"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+
+[[SimpleTraits]]
+deps = ["InteractiveUtils", "MacroTools"]
+git-tree-sha1 = "2bdf3b6300a9d66fe29ee8bb51ba100c4df9ecbc"
+uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
+version = "0.9.1"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[StaticArrays]]
+deps = ["LinearAlgebra", "Random", "Statistics"]
+git-tree-sha1 = "5a3bcb6233adabde68ebc97be66e95dcb787424c"
+uuid = "90137ffa-7385-5640-81b9-e52037218182"
+version = "0.12.1"
+
+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[TranscodingStreams]]
+deps = ["Random", "Test"]
+git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c"
+uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
+version = "0.9.5"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[XML2_jll]]
+deps = ["Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
+git-tree-sha1 = "ed5603a695aefe3e9e404fc7b052e02cc72cfab6"
+uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
+version = "2.9.9+1"
+
+[[Zlib_jll]]
+deps = ["Libdl", "Pkg"]
+git-tree-sha1 = "fd36a6739e256527287c5444960d0266712cd49e"
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.11+8"

Project.toml

@@ -0,0 +1,24 @@
+name = "GraphIO"
+uuid = "2f0f772a-13f1-4a16-8943-390acdf9ae6b"
+authors = ["Seth Bromberger"]
+version = "0.4.0"
+
+[deps]
+CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
+LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
+ParserCombinator = "fae87a5f-d1ad-5cf0-8f61-c941e1580b46"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
+
+[compat]
+CodecZlib = "^0.6"
+EzXML = "^1.1"
+LightGraphs = "^1.3"
+MetaGraphs = "^0.6"
+ParserCombinator = "^2.0"
+Requires = "^1.0"
+SimpleTraits = "^0.9"
+

src/GEXF/Gexf.jl

@@ -2,6 +2,7 @@ module GEXF
 
 using GraphIO.EzXML
 using LightGraphs
+using MetaGraphs
 using LightGraphs: AbstractGraph, AbstractGraphFormat
 
 import LightGraphs: savegraph
@@ -50,6 +51,7 @@ function savegexf(io::IO, g::LightGraphs.AbstractGraph, gname::String)
     return 1
 end
 
-savegraph(io::IO, g::AbstractGraph, gname::String, ::GEXFFormat) = savegexf(io, g, gname)
 
+
+include("metagraphs.jl")
 end #module

src/GEXF/metagraphs.jl

@@ -0,0 +1,91 @@
+using MetaGraphs
+
+function idandtypes(prs)
+    k2id = Dict{Symbol,Int}()
+    k2type = Dict{Symbol,Type}()
+    i = 1
+    for vs in values(prs)
+        for (k,v) in (vs)
+            if haskey(k2id, k)
+                if k2type[k] != typeof(v)
+                    k2type[k] = promote_type(k2type[k],typeof(v))
+                end
+            else
+                k2id[k] = i 
+                i += 1
+                k2type[k] = typeof(v)
+            end 
+        end
+    end
+    return(k2id, k2type)
+end
+
+type2string(::Type{T}) where {T<:Integer} = "integer"
+type2string(::Type{T}) where {T<:AbstractFloat} = "double"
+type2string(::Type{T}) where {T<:Char} = "string"
+type2string(::Type{T}) where {T<:AbstractString} = "string"
+
+function exportattributes(xg, prs, element_type)
+    (k2id, k2type) = idandtypes(prs)
+    if !isempty(k2id)
+        xattrs = addelement!(xg, "attributes")
+        xattrs["class"] = element_type
+        for (k,i) in k2id
+            xat=addelement!(xattrs, "attribute")
+            xat["id"] = i
+            xat["title"] = k
+            xat["type"] = type2string(k2type[k])
+        end
+    end
+    k2id
+end
+
+function add_properties!(xv, ks, prs)
+    isempty(prs) && return
+    av = addelement!(xv, "attvalues")
+    for (k,v) in prs
+        av = addelement!(av, "attvalue")
+        av["for"] = ks[k]
+        av["value"] = v
+    end
+end
+
+function savegexf(io::IO, g::MetaGraph, gname::String)
+    xdoc = XMLDocument()
+    xroot = setroot!(xdoc, ElementNode("gexf"))
+    xroot["xmlns"] = "http://www.gexf.net/1.2draft"
+    xroot["version"] = "1.2"
+    xroot["xmlns:xsi"] = "http://www.w3.org/2001/XMLSchema-instance"
+    xroot["xsi:schemaLocation"] = "http://www.gexf.net/1.2draft/gexf.xsd"
+
+    xmeta = addelement!(xroot, "meta")
+    addelement!(xmeta, "description", gname)
+    xg = addelement!(xroot, "graph")
+    strdir = is_directed(g) ? "directed" : "undirected"
+    xg["defaultedgetype"] = strdir
+
+
+    vks = exportattributes(xg, g.vprops, "node")
+    eks = exportattributes(xg, g.eprops, "edge")
+
+    xnodes = addelement!(xg, "nodes")
+    for v in vertices(g)
+        xv = addelement!(xnodes, "node")
+        xv["id"] = "$(v-1)"
+        add_properties!(xv, vks, props(g, v))
+    end
+
+    xedges = addelement!(xg, "edges")
+    m = 0
+    for e in LightGraphs.edges(g)
+        xe = addelement!(xedges, "edge")
+        xe["id"] = "$m"
+        xe["source"] = "$(src(e)-1)"
+        xe["target"] = "$(dst(e)-1)"
+        add_properties!(xe, eks, props(g, e))
+        m += 1
+    end
+
+    prettyprint(io, xdoc)
+    return 1
+end

src/GraphIO.jl

@@ -1,7 +1,6 @@
 module GraphIO
 
 using Requires
-
 #=
     NOTE: This is a temporary fix until we can have multiple sub-packages with their own 
     requirements in a single repository.