Added functionality to save graphs in DOT format #23

abhinavmehndiratta · 2018-12-16T18:36:09Z

julia> using ParserCombinator,LightGraphs,GraphIO

julia> x = SimpleGraph(5,10)
{5, 10} undirected simple Int64 graph

julia> y = SimpleDiGraph(5,10)
{5, 10} directed simple Int64 graph

julia> savegraph("/home/abhinav/undirected.dot",x,"undg",DOTFormat())
┌ Warning: `GraphIO.DOTFormat`  has been moved to submodule `GraphIO.DOT` and needs `ParserCombinator.jl` to be imported first. I.e. use
│     using ParserCombinator
│     GraphIO.DOT.DOTFormat()
│   caller = top-level scope at none:0
└ @ Core none:0
1

julia> savegraph("/home/abhinav/directed.dot",y,"dg",DOTFormat())
┌ Warning: `GraphIO.DOTFormat`  has been moved to submodule `GraphIO.DOT` and needs `ParserCombinator.jl` to be imported first. I.e. use
│     using ParserCombinator
│     GraphIO.DOT.DOTFormat()
│   caller = top-level scope at none:0
└ @ Core none:0
1

julia> p = loadgraph("/home/abhinav/undirected.dot","undg",DOTFormat())
┌ Warning: `GraphIO.DOTFormat`  has been moved to submodule `GraphIO.DOT` and needs `ParserCombinator.jl` to be imported first. I.e. use
│     using ParserCombinator
│     GraphIO.DOT.DOTFormat()
│   caller = top-level scope at none:0
└ @ Core none:0
{5, 10} undirected simple Int64 graph

julia> q = loadgraph("/home/abhinav/directed.dot","dg",DOTFormat())
┌ Warning: `GraphIO.DOTFormat`  has been moved to submodule `GraphIO.DOT` and needs `ParserCombinator.jl` to be imported first. I.e. use
│     using ParserCombinator
│     GraphIO.DOT.DOTFormat()
│   caller = top-level scope at none:0
└ @ Core none:0
{5, 10} directed simple Int64 graph

julia> p == x
true

julia> q == y
true

codecov · 2018-12-16T18:40:38Z

Codecov Report

Merging #23 into master will decrease coverage by 15.99%.
The diff coverage is 10.34%.

@@           Coverage Diff            @@
##           master      #23    +/-   ##
========================================
- Coverage   99.67%   83.67%   -16%     
========================================
  Files          10       11     +1     
  Lines         304      435   +131     
========================================
+ Hits          303      364    +61     
- Misses          1       71    +70

Impacted Files	Coverage Δ
src/DOT/Dot.jl	`55.17% <10.34%> (-44.83%)`	⬇️
src/GraphIO.jl	`44.44% <0%> (-55.56%)`	⬇️
src/LGCompressed/LGCompressed.jl	`55.55% <0%> (-33.34%)`	⬇️
src/NET/Net.jl	`88.88% <0%> (-11.12%)`	⬇️
src/Edgelist/Edgelist.jl	`91.66% <0%> (-8.34%)`	⬇️
src/CDF/Cdf.jl	`93.54% <0%> (-6.46%)`	⬇️
src/Graph6/Graph6.jl	`94.18% <0%> (-5.82%)`	⬇️
src/GEXF/Gexf.jl	`96.42% <0%> (-3.58%)`	⬇️
src/GraphML/GraphML.jl	`97.4% <0%> (-2.6%)`	⬇️
src/GML/Gml.jl	`100% <0%> (ø)`	⬆️
... and 1 more

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codecov · 2018-12-16T18:40:39Z

Codecov Report

Merging #23 into master will decrease coverage by 8.05%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master      #23      +/-   ##
==========================================
- Coverage   99.67%   91.62%   -8.06%     
==========================================
  Files          10       11       +1     
  Lines         304      358      +54     
==========================================
+ Hits          303      328      +25     
- Misses          1       30      +29

Impacted Files	Coverage Δ
src/DOT/Dot.jl	`100% <100%> (ø)`	⬆️
src/LGCompressed/LGCompressed.jl	`44.44% <0%> (-44.45%)`	⬇️
src/GraphIO.jl	`75% <0%> (-25%)`	⬇️
src/Edgelist/Edgelist.jl	`94.73% <0%> (-5.27%)`	⬇️
src/CDF/Cdf.jl	`95.65% <0%> (-4.35%)`	⬇️
src/Graph6/Graph6.jl	`98.43% <0%> (-1.57%)`	⬇️
src/GraphML/GraphML.jl	`100% <0%> (ø)`	⬆️
src/deprecations.jl	`0% <0%> (ø)`

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simonschoelly

Good thing we get this functionality. As you see, you are getting some warnings. This is, because DOTFormat has been moved to the submodule GraphIO.DOT.DOTFormat. So you either have to write DOT.DOTFormat. or using GraphIO.DOT: DOTFormat.

I wonder if this would be a good opportunity to add the ability to add the ability to attach labels to vertices and edges, as this is not too difficult with this format. We could do this with optional keyword arguments. What do you think @sbromberger ?

simonschoelly · 2018-12-16T18:56:08Z

src/DOT/Dot.jl

+                continue
+            end
+            s = string(n)
+            edg = edg * "\n\t" * string(u) * " -> {" * s[2:length(s)-1] * "}"


Thats a clever trick, but the output of string(n) changes slightly in the future, this might break. consider doing something like join(map(string, outneighbors(g, u)), ", ") instead.

simonschoelly · 2018-12-16T18:56:47Z

src/DOT/Dot.jl

+    edg = ""
+    if isdir
+        for u in LightGraphs.vertices(g)
+            n = LightGraphs.outneighbors(g, u)


n is not a good name here, usually people assume that this would be an integer.

simonschoelly · 2018-12-16T19:02:32Z

src/DOT/Dot.jl

+        for e in LightGraphs.edges(g)
+            source = string(LightGraphs.src(e))
+            dest = string(LightGraphs.dst(e))
+            edg = edg * "\n\t" * source * " -- " * dest


The problem here is that you use * to build a large string. This creates a lot of unnecessary allocations and will become really slow when the graph gets big. Its better to work with IOBuffers or write each line directly to io as soon as you have finished creating it. In fact you can use println(io, "some string"), so you will not have to insert \n manually.

abhinavmehndiratta · 2018-12-16T19:57:51Z

using ParserCombinator,LightGraphs,GraphIO
x = SimpleGraph(5,10)
y = SimpleDiGraph(5,2)
savegraph("/home/abhinav/undirected.dot",x,"undg",GraphIO.DOT.DOTFormat())
savegraph("/home/abhinav/directed.dot",y,"dg",GraphIO.DOT.DOTFormat())
p = loadgraph("/home/abhinav/undirected.dot","undg",GraphIO.DOT.DOTFormat())
q = loadgraph("/home/abhinav/directed.dot","dg",GraphIO.DOT.DOTFormat())
println(p == x)
println(q == y)

Output -

true
true

sbromberger · 2018-12-16T20:24:32Z

I wonder if this would be a good opportunity to add the ability to add the ability to attach labels to vertices and edges, as this is not too difficult with this format. We could do this with optional keyword arguments. What do you think @sbromberger ?

I think this might be better as a method forMetaGraphs.jl..

purchawek · 2018-12-21T09:58:30Z

Hi, I'm not a contributor here, but I'm waiting for this functionality to be added and I just took a look on the code you've submitted.

This is a fairly straightforward functionality and I'm wondering why you keep all the logic in a single function. In line 14 you distinguish directed and undirected graphs, and hence use the variable isdir to handle these two mutually exclusive cases. Wouldn't it be nicer to have two separate methods for directed and undirected graphs and call one of them accordingly to the value stored in isdir?

simonschoelly · 2018-12-21T14:38:07Z

I wonder if this would be a good opportunity to add the ability to add the ability to attach labels to vertices and edges, as this is not too difficult with this format. We could do this with optional keyword arguments. What do you think @sbromberger ?

I think this might be better as a method forMetaGraphs.jl..

There are two reasons, why I think it might be a good idea to do that here:

DOT is often used with graphviz for plotting, this would mean, that we would have to convert to a MetaGraph first, if we want to put labels on edges and vertices.
If we had the functionality to add labels here, then we could base the code MetaGraphs.jl on it. Otherwise we would have to do an implementation for all other packages that support labels on edges and vertices.

simonschoelly · 2019-03-22T19:50:05Z

We really should make some progress here. Lets skip the issue with the metadata, that can be added later. I think in your current code, isolated vertices will not be added to the dotfile? Can you fix that?

abhinavmehndiratta · 2019-03-22T20:37:06Z

We really should make some progress here. Lets skip the issue with the metadata, that can be added later. I think in your current code, isolated vertices will not be added to the dotfile? Can you fix that?

Isolated vertices are added. The problem is that when you save the DOT file and load it again the graphs will not be the same because of this -

GraphIO.jl/src/DOT/Dot.jl

Line 49 in b79931c

nodedict = Dict(zip(collect(Parsers.DOT.nodes(pg)), 1:nvg))

simonschoelly · 2019-03-23T11:43:16Z

You are right, I totally forgot about that. But your code outputs the graph in the right order and it is the importer that messes that up? Because in that case, we don't have to fix it here.

simonschoelly · 2019-03-23T11:47:01Z

Can you add some tests? We can get around the issue that the vertex order is messed up in the importer by either using vertex-transitive graphs for testing or by using the isomorphism algorithms for reordering.

abhinavmehndiratta · 2019-03-23T14:36:10Z

You are right, I totally forgot about that. But your code outputs the graph in the right order and it is the importer that messes that up? Because in that case, we don't have to fix it here.

Yes the DOT parser returns nodes in random order, so the loaded graph is not the same but yes the saved graph is correct.

abhinavmehndiratta · 2019-03-23T14:39:29Z

Can you add some tests? We can get around the issue that the vertex order is messed up in the importer by either using vertex-transitive graphs for testing or by using the isomorphism algorithms for reordering.

If I understand correctly does that mean checking if the loaded graph is isomorphic to the original saved graph in the tests ? But the problem will still remain, right ? I mean is it only for testing ?

abhinavmehndiratta · 2019-03-23T14:43:07Z

We could fix this problem for LightGraphs only btw, like b79931c I was doing before, but then it is not generalized.

simonschoelly · 2019-03-23T14:44:25Z

Yes, only for testing. Maybe also add a comment there, why we are doing this.

Let's think about what would be correct for the importer in another issue/pr, so we can finally merge this.

abhinavmehndiratta · 2019-03-23T14:45:41Z

Yes, only for testing. Maybe also add a comment there, why we are doing this.

Let's think about what would be correct for the importer in another issue/pr, so we can finally merge this.

Okay I'll add some tests then.

abhinavmehndiratta · 2019-03-24T18:21:29Z

I have added the tests but code coverage seems to be wrong.

src/DOT/Dot.jl

simonschoelly · 2020-03-08T23:34:06Z

Ouch, this got completely forgotten. Maybe you can implement that thing that I suggested and then rebase on master. Then lets see if code coverage still complains..

Co-Authored-By: Simon Schoelly <[email protected]>

abhinavmehndiratta · 2020-03-12T14:50:58Z

The diff coverage seems fine.

sbromberger · 2020-05-10T19:52:15Z

Are we good to merge this?

Added function to save graphs in DOT format

d9d86b8

simonschoelly reviewed Dec 16, 2018

View reviewed changes

Using println instead of concatenation and removed labels

31c855f

using old approach for nodedict

b79931c

abhinavmehndiratta added 2 commits March 24, 2019 23:25

add tests for write DOT

65af08c

add test for single graph

0f6faca

add more tests

77c5ca7

simonschoelly reviewed Mar 8, 2020

View reviewed changes

src/DOT/Dot.jl Outdated Show resolved Hide resolved

abhinavmehndiratta and others added 2 commits March 11, 2020 10:51

shortcircuit if statement

da71640

Co-Authored-By: Simon Schoelly <[email protected]>

correct whitespace

1165562

sbromberger merged commit 6db4c3d into JuliaGraphs:master May 10, 2020

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Added functionality to save graphs in DOT format #23

Added functionality to save graphs in DOT format #23

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Added functionality to save graphs in DOT format #23

Added functionality to save graphs in DOT format #23

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