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+*)
+
+(*** include:csvSample ***)
+
+
+(**
+
+
+
+*)
+
+(**
+###Data aquisition
+
+First we parse the .obo file using BioFSharps Obo parser:
+
+*)
+
+open FSharpAux
+open FSharpAux.IO
+open BioFSharp
+open BioFSharp.IO
+open BioFSharp.IO.Obo
+
+let readFile path =
+ FileIO.readFile path
+ |> Obo.parseOboTerms
+ |> Seq.toList
+
+(***do-not-eval***)
+let goObo = readFile @"go.obo"
+
+(**
+
+### Preparing nodes and edges
+
+We define nodes as GO terms as our nodes and edges as Is-A relations between those terms. This will result in a network that shows how the knowledgebase is structured.
+There are a few interesting thigs that can be visualized by this:
+
+ * **The most descriptive terms**: The nodes with the highest In-Degree are the terms which describe the most knowledge in the network.
+ Maybe we can also infere from this what the main fields of (geneomic) biological research are.
+ * **Sub graphs of the network** may show that there are different well described knowledge types that are highly differentiaded from each other
+ * **Connectivity between hubs**: Terms that connect subgraphs or hubs and act as 'knowledge glue'
+
+However, there is much more information in the obi file than these relationships. Visualizing other relationships is a topic for another day.
+
+*)
+
+open FSharpGephiStreamer
+open FSharpGephiStreamer.Colors
+
+(***do-not-eval***)
+/// Simplified GO Term as node
+type GONode = {
+ //GO term (e.g. "GO:0000001")
+ Id : string
+ //full term description e.g. "RNA polymerase I transcription factor complex"
+ TermDescription : string
+ //e.g. "biological process"
+ NameSpace : string
+ //The color for the node
+ Color : Colors.Color
+ }
+
+/// Creates GONode
+let createGONode id descr nameSpace col =
+ {Id = id; TermDescription = descr; NameSpace = nameSpace ; Color = col}
+
+/// Represents the Is_A relationship of GO terms as a directed edge
+type GOEdge = {
+ Id : int
+ Source : string
+ Target : string
+ TargetColor : Colors.Color
+}
+
+/// Creates GOEdge
+let createGOEdge i source target tc = {Id = i; Source = source; Target = target; TargetColor = tc}
+
+
+///Node list containing all GO terms
+let goNodes =
+ goObo
+ |> List.map (fun x -> (createGONode x.Id x.Name x.Namespace (Colors.Table.StatisticalGraphics24.getRandomColor())))
+
+
+///Edge list containing all Is-A relationships in the knowledge base
+let goEdges =
+ goObo
+ //ignore terms that have no Is-A relationship to any term
+ |> List.filter (fun x -> not (List.isEmpty x.IsA))
+ |> List.map (fun x ->
+ [for target in x.IsA do
+ yield ( x.Id,
+ target ,
+ //ensure edges have the color of the node they target;
+ (goNodes |> List.find(fun node -> node.Id = target) ).Color)
+ ])
+ //Aggregate resulting edges in a single list
+ |> List.concat
+ |> List.mapi (fun i (sourceId, targetId, col) -> createGOEdge (i+1) sourceId targetId col)
+
+(**
+### Streaming to gephi
+
+The `Grammar` module provides a set of rules that will convert the streamed data into JSON objects which gephi will understand.
+To stream the nodes and edges to Gephi, we need a converter function for both. This function will take:
+ * The edge/node
+ * A list of Grammar attributes that define the mapping of attributes of the data to Gephi-readable attributes
+
+We then use functional compostion with the `Streamer.addNode`/`Streamer.addEdge` functions to create our final addNode/Edge functions.
+
+*)
+
+(***do-not-eval***)
+let addOboNode (node:GONode) =
+
+ let nodeConverter (node:GONode) =
+ [
+ Grammar.Attribute.Label (sprintf "%s | %s {%s}" node.Id node.TermDescription node.NameSpace);
+ Grammar.Attribute.Size 10.;
+ Grammar.Attribute.Color node.Color;
+ Grammar.Attribute.UserDef ("UserData",node.TermDescription);
+ ]
+ Streamer.addNode nodeConverter node.Id node
+
+
+let addOboEdge (edge:GOEdge) =
+
+ let edgeConverter (edge:GOEdge) =
+ [
+ Grammar.Attribute.Size 1.;
+ Grammar.Attribute.EdgeType Grammar.EdgeDirection.Directed;
+ Grammar.Attribute.Color edge.TargetColor ;
+ ]
+
+ Streamer.addEdge edgeConverter edge.Id edge.Source edge.Target edge
+
+
+goNodes |> List.map addOboNode
+goEdges |> List.map addOboEdge
+
+(**
+Thats it. in roughly 40 lines of code we streamed a complete knowledge graph with 47345 nodes and 77187 edges to gephi. The network is now ready to be explored.
+
+*)
+
+(*** define:csvSample***)
+open System.IO
+open System.Text
+
+let readFromFile (file:string) =
+ seq {use textReader = new StreamReader(file, Encoding.Default)
+ while not textReader.EndOfStream do
+ yield textReader.ReadLine()}
+
+let nodes =
+ readFromFile (__SOURCE_DIRECTORY__ + "/data/goNodeList.csv")
+ |> List.ofSeq
+ |> List.map (fun n -> let tmp = n.Split([|','|])
+ createGONode tmp.[0] tmp.[1] tmp.[2] (Colors.Table.StatisticalGraphics24.getRandomColor()))
+
+let edges =
+ readFromFile (__SOURCE_DIRECTORY__ + "/data/goEdgeList.csv") |> List.ofSeq
+ |> List.ofSeq
+ |> List.map (fun n -> let tmp = n.Split([|','|])
+ createGOEdge (tmp.[0] |> int) tmp.[1] tmp.[2] (nodes |> List.find(fun n -> n.Id = tmp.[2])).Color)
+(**
+
+# Results
+
+## The network
+
+After applying some styles in the preview section (e.g. black background, rounded edges) the final rendered network looks like this:
+
+
+
+## Network sections
+
+By eye, there are 9 large communities in the network, clustering knowledge about the following processes/entities (click to view a close-up):
+
+
+
+
+## Metrics
+
+###Average Degree & Degree distribution
+
+
+
+The average Degree is 1.63. The degree distribution is highly right-skewed (meaning many nodes have a low degree, and there exist hubs with high degree). This is a property of a real network.
+
+###Modularity
+
+Calculating the network modularity with a low resolution, the large communities correlate well with the previous by-eye observation, although some of these communities split into large sub-communities:
+The overall modularity of the network with a resolution of 3 is 0.89 (high modularity).
+
+Below is the network with nodes colored by their community membership:
+
+
+
+# Close up of some communities
+
+## Binding
+
+Back to overview
+
+
+
+## Transferases
+
+Back to overview
+
+
+
+## Regulation
+
+Back to overview
+
+
+
+## Protein-Complex
+
+Back to overview
+
+
+
+## Metabolic-Processes
+
+Back to overview
+
+
+
+## Oxireductases
+
+Back to overview
+
+
+
+## Intracellular-Transport
+
+Back to overview
+
+
+
+## Reproduction
+
+Back to overview
+
+
+
+## Transmembrane-Transport
+
+Back to overview
+
+
+
+*)
\ No newline at end of file
diff --git a/docsrc/content/index.fsx b/docsrc/content/index.fsx
index 1172560..5a28464 100644
--- a/docsrc/content/index.fsx
+++ b/docsrc/content/index.fsx
@@ -1,67 +1,32 @@
(*** hide ***)
// This block of code is omitted in the generated HTML documentation. Use
// it to define helpers that you do not want to show in the documentation.
-#I "../../bin"
+#I "../../bin/FSharpGephiStreamer/net47"
(**
-FSharpGephiStreamer
-======================
+# FSharpGephiStreamer
-Documentation
+FSharpGephiStreamer is intended to close the gap between F# and the functionality of the [Gephi software project](https://gephi.org/), integrating network visualization
+power of gephi into any kind of data science workflow designed in F#. It leverages the functionality of the [graph streaming plugin](https://gephi.org/plugins/#/plugin/graphstreaming) of the It uses a short Grammar which makes it possible to convert any
+kind of Object to nodes and any kind of relationship between these objects to edges of a graph. This is especially useful because network
+science is independent from specific data structures/types.
-
-
-
+
-Example
--------
+# Ressources
-This example demonstrates using a function defined in this sample library.
+## Installation
-*)
-#r "FSharpGephiStreamer.dll"
-open FSharpGephiStreamer
+See how to [setup FSharpGephiStreamer](InstallationInstructions.html)
-printfn "hello = %i" <| Library.hello 0
+## Docs
-(**
-Some more info
-
-Samples & documentation
------------------------
-
-The library comes with comprehensible documentation.
-It can include tutorials automatically generated from `*.fsx` files in [the content folder][content].
-The API reference is automatically generated from Markdown comments in the library implementation.
-
- * [Tutorial](tutorial.html) contains a further explanation of this sample library.
-
- * [API Reference](reference/index.html) contains automatically generated documentation for all types, modules
- and functions in the library. This includes additional brief samples on using most of the
- functions.
-
-Contributing and copyright
---------------------------
+ * See how to [convert any kind of nodes/edges](Grammar.html) to gephi readable objects using the `Grammar` module
+ * See how to [stream graph data to gephi](Streaming.html)
+ * Check out the [API Reference](https://csbiology.github.io/FSharpGephiStreamer/reference/index.html) for information about types/functions in this library
-The project is hosted on [GitHub][gh] where you can [report issues][issues], fork
-the project and submit pull requests. If you're adding a new public API, please also
-consider adding [samples][content] that can be turned into a documentation. You might
-also want to read the [library design notes][readme] to understand how it works.
+## Examples
-The library is available under Public Domain license, which allows modification and
-redistribution for both commercial and non-commercial purposes. For more information see the
-[License file][license] in the GitHub repository.
+ * [Exploratory analysis of the Gene Ontology knowledgebase](exampleAnalysis.html)
- [content]: https://github.com/fsprojects/FSharpGephiStreamer/tree/master/docs/content
- [gh]: https://github.com/fsprojects/FSharpGephiStreamer
- [issues]: https://github.com/fsprojects/FSharpGephiStreamer/issues
- [readme]: https://github.com/fsprojects/FSharpGephiStreamer/blob/master/README.md
- [license]: https://github.com/fsprojects/FSharpGephiStreamer/blob/master/LICENSE.txt
-*)
+*)
\ No newline at end of file
diff --git a/docsrc/content/tutorial.fsx b/docsrc/content/tutorial.fsx
deleted file mode 100644
index 3a34693..0000000
--- a/docsrc/content/tutorial.fsx
+++ /dev/null
@@ -1,19 +0,0 @@
-(*** hide ***)
-// This block of code is omitted in the generated HTML documentation. Use
-// it to define helpers that you do not want to show in the documentation.
-#I "../../bin"
-
-(**
-Introducing your project
-========================
-
-Say more
-
-*)
-#r "FSharpGephiStreamer.dll"
-open FSharpGephiStreamer
-
-Library.hello 0
-(**
-Some more info
-*)
diff --git a/docsrc/files/img/AverageDegree.jpg b/docsrc/files/img/AverageDegree.jpg
new file mode 100644
index 0000000..3d7223a
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diff --git a/docsrc/files/img/Communities.png b/docsrc/files/img/Communities.png
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new file mode 100644
index 0000000..c749a9e
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diff --git a/docsrc/files/img/MetabolicNetwork.png b/docsrc/files/img/MetabolicNetwork.png
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index 0000000..48c7798
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diff --git a/docsrc/files/img/OboNetworkMeta.png b/docsrc/files/img/OboNetworkMeta.png
new file mode 100644
index 0000000..55dc6a9
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diff --git a/docsrc/files/img/OboNetworkOverview.jpg b/docsrc/files/img/OboNetworkOverview.jpg
new file mode 100644
index 0000000..870a49d
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diff --git a/docsrc/files/img/OboNetworkOverview.png b/docsrc/files/img/OboNetworkOverview.png
new file mode 100644
index 0000000..580c78f
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diff --git a/docsrc/files/img/OxireductasesNetwork.png b/docsrc/files/img/OxireductasesNetwork.png
new file mode 100644
index 0000000..a1cefe8
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diff --git a/docsrc/files/img/ProteinComplexNetwork.png b/docsrc/files/img/ProteinComplexNetwork.png
new file mode 100644
index 0000000..713ac46
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diff --git a/docsrc/files/img/RegulationNetwork.png b/docsrc/files/img/RegulationNetwork.png
new file mode 100644
index 0000000..6b3357f
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diff --git a/docsrc/files/img/TransferasesNetwork.png b/docsrc/files/img/TransferasesNetwork.png
new file mode 100644
index 0000000..b7d664d
Binary files /dev/null and b/docsrc/files/img/TransferasesNetwork.png differ
diff --git a/docsrc/files/img/TransmembraneTransportNetwork.png b/docsrc/files/img/TransmembraneTransportNetwork.png
new file mode 100644
index 0000000..8ad70b4
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diff --git a/docsrc/files/img/TransportNetwork.png b/docsrc/files/img/TransportNetwork.png
new file mode 100644
index 0000000..caffaf7
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diff --git a/docsrc/files/img/pluginInstallation.jpg b/docsrc/files/img/pluginInstallation.jpg
new file mode 100644
index 0000000..f13e9ff
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diff --git a/docsrc/files/styles/CSBStyles.css b/docsrc/files/styles/CSBStyles.css
new file mode 100644
index 0000000..5525b31
--- /dev/null
+++ b/docsrc/files/styles/CSBStyles.css
@@ -0,0 +1,172 @@
+table.pre {
+ border: hidden;
+ overflow-x: auto;
+ white-space: nowrap;
+ display: block;
+}
+
+ table.pre::-webkit-scrollbar-track {
+ -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.3);
+ border-radius: 5px;
+ background-color: #212d30;
+ }
+
+ table.pre::-webkit-scrollbar {
+ height: 8px;
+ background-color: #212d30;
+ border-radius: 5px
+ }
+
+ table.pre::-webkit-scrollbar-thumb {
+ border-radius: 5px;
+ -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,.3);
+ background-color: #80b0b0;
+ }
+
+pre {
+ border: hidden;
+ overflow-x: auto;
+}
+
+ pre::-webkit-scrollbar-track {
+ -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.3);
+ border-radius: 5px;
+ background-color: #212d30;
+ }
+
+ pre::-webkit-scrollbar {
+ height: 8px;
+ background-color: #212d30;
+ border-radius: 5px
+ }
+
+ pre::-webkit-scrollbar-thumb {
+ border-radius: 5px;
+ -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,.3);
+ background-color: #80b0b0;
+ }
+
+#main {
+ text-align: justify;
+}
+
+ #main h2 {
+ margin: 10px 0px 10px 0px;
+ }
+
+ #main h1 {
+ text-align:left;
+ }
+
+#responsiveTable {
+ overflow-x: auto;
+}
+
+ #responsiveTable::-webkit-scrollbar-track {
+ -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.3);
+ border-radius: 5px;
+ background-color: #212d30;
+ }
+
+ #responsiveTable::-webkit-scrollbar {
+ height: 8px;
+ background-color: #212d30;
+ border-radius: 5px
+ }
+
+ #responsiveTable::-webkit-scrollbar-thumb {
+ border-radius: 5px;
+ -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,.3);
+ background-color: #80b0b0;
+ }
+
+ #responsiveTable p {
+ margin: 0px 0px 0px 0px;
+ }
+
+ #responsiveTable table {
+ border: 2px solid #2E75B6;
+ border-radius: 50px;
+ }
+
+ #responsiveTable tr:nth-child(even) {
+ background-color: #BDD7EE;
+ }
+
+ #responsiveTable tr {
+ border: 1px solid #2E75B6;
+ }
+
+ #responsiveTable th {
+ background-color: #2E75B6;
+ color: white;
+ }
+
+ #responsiveTable th, td {
+ text-align: left;
+ padding: 0px 10px 0px 10px;
+ }
+
+.fileExamples {
+ overflow-x: auto;
+ white-space: nowrap;
+ display: block;
+}
+
+ .fileExamples pre {
+ background-color: white;
+ color: black;
+ }
+
+ .fileExamples::-webkit-scrollbar-track {
+ -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.3);
+ border-radius: 5px;
+ background-color: #212d30;
+ }
+
+ .fileExamples::-webkit-scrollbar {
+ height: 8px;
+ background-color: #212d30;
+ border-radius: 5px
+ }
+
+ .fileExamples::-webkit-scrollbar-thumb {
+ border-radius: 5px;
+ -webkit-box-shadow: inset 0 0 6px rgba(0,0,0,.3);
+ background-color: #80b0b0;
+ }
+
+#exampleToggle {
+ border-color: #2E75B6;
+}
+
+#SourceCode, #Author, #APILink {
+ text-align: center;
+ color: #2E75B6;
+ padding: 2px 6px 2px 6px;
+ /*border-radius: 25px;
+ border: 2px solid #2E75B6;*/
+ text-decoration: none;
+}
+
+
+
+ #Author:hover, #SourceCode:hover, #APILink:hover {
+ background-color: #2E75B6;
+ color: white;
+ }
+
+
+
+table.HeadAPI {
+ width: 100%
+}
+
+td.Head {
+ padding: 0px;
+}
+
+td.API {
+ padding: 0px;
+ text-align: right;
+}
diff --git a/docsrc/tools/templates/template.cshtml b/docsrc/tools/templates/template.cshtml
index 1ae4a1b..121cf91 100644
--- a/docsrc/tools/templates/template.cshtml
+++ b/docsrc/tools/templates/template.cshtml
@@ -1,24 +1,24 @@
-
-
+
+
-
-
-
- The FSharpGephiStreamer library can be installed from NuGet:
-
- PM> Install-Package FSharpGephiStreamer-
@@ -43,9 +43,16 @@
Source Code on GitHub
License
Release Notes
-
+
Getting started
- Sample tutorial
+ Installation instructions
+
+ Data preparation & streaming
+ Converting nodes and edges
+ Streaming
+
+ Examples
+ Exploratory analysis of the Gene Ontology knowledgebase
Documentation
API Reference
diff --git a/lib/ForDocs/BioFSharp.IO.dll b/lib/ForDocs/BioFSharp.IO.dll
new file mode 100644
index 0000000..90d13d6
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diff --git a/lib/ForDocs/BioFSharp.dll b/lib/ForDocs/BioFSharp.dll
new file mode 100644
index 0000000..1d24757
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diff --git a/lib/ForDocs/FSharpAux.IO.dll b/lib/ForDocs/FSharpAux.IO.dll
new file mode 100644
index 0000000..17a5e1a
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diff --git a/lib/ForDocs/FSharpAux.dll b/lib/ForDocs/FSharpAux.dll
new file mode 100644
index 0000000..057a8b6
Binary files /dev/null and b/lib/ForDocs/FSharpAux.dll differ
diff --git a/src/FSharpGephiStreamer/AssemblyInfo.fs b/src/FSharpGephiStreamer/AssemblyInfo.fs
index 15ef113..e9eed1c 100644
--- a/src/FSharpGephiStreamer/AssemblyInfo.fs
+++ b/src/FSharpGephiStreamer/AssemblyInfo.fs
@@ -5,8 +5,8 @@ open System.Reflection
[]
[]
[]
-[]
-[]
+[]
+[]
[]
do ()
@@ -14,6 +14,6 @@ module internal AssemblyVersionInformation =
let [] AssemblyTitle = "FSharpGephiStreamer"
let [] AssemblyProduct = "FSharpGephiStreamer"
let [] AssemblyDescription = "FSharp functions for streaming graph data to gephi a graph visualization tool"
- let [] AssemblyVersion = "1.0.0"
- let [] AssemblyFileVersion = "1.0.0"
+ let [] AssemblyVersion = "1.1.0"
+ let [] AssemblyFileVersion = "1.1.0"
let [] AssemblyConfiguration = "Release"
diff --git a/src/FSharpGephiStreamer/Color.fs b/src/FSharpGephiStreamer/Color.fs
index e852917..c44bcff 100644
--- a/src/FSharpGephiStreamer/Color.fs
+++ b/src/FSharpGephiStreamer/Color.fs
@@ -1,20 +1,24 @@
namespace FSharpGephiStreamer
+///Functions and types for color coding, decoding and conversions of hex colors
module Hex =
open System
+ ///Converts integer to hex based character (e.g. 1 -> '1', 11 -> 'B')
[]
let toHexDigit n =
if n < 10 then char (n + 0x30) else char (n + 0x37)
+ ///Converts a hex based character to an integer (e.g. '1' -> 1, 'B' -> 11)
[]
let fromHexDigit c =
if c >= '0' && c <= '9' then int c - int '0'
elif c >= 'A' && c <= 'F' then (int c - int 'A') + 10
elif c >= 'a' && c <= 'f' then (int c - int 'a') + 10
else raise <| new ArgumentException()
-
+
+ ///Encodes a color byte array to a hex string with the given prefix
[]
let encode (prefix:string) (color:byte array) =
let hex = Array.zeroCreate (color.Length * 2)
@@ -29,6 +33,7 @@ module Hex =
// else new String(hex)
[]
+ ///Decodes a color byte array from a hex string
let decode (s:string) =
match s with
| null -> nullArg "s"
@@ -50,7 +55,7 @@ module Hex =
buf
//http://www.niwa.nu/2013/05/math-behind-colorspace-conversions-rgb-hsl/
-/// Represents an ARGB (alpha, red, green, blue) color
+///Module to create and manipulate ARGB colors
module Colors =
/// Color component ARGB
@@ -60,6 +65,7 @@ module Colors =
| G of byte
| B of byte
+ /// returns the value hold by a color component
let getValueFromCC cc =
match cc with
| A v -> v
@@ -67,7 +73,7 @@ module Colors =
| G v -> v
| B v -> v
- /// Color structure
+ ///Represents an ARGB (alpha, red, green, blue) color
type Color = {
/// The alpha component value of this Color structure.
A : byte
@@ -79,18 +85,19 @@ module Colors =
B : byte
}
-
+ ///returns the maximum value of the R, G, and B components of a color
let maxRGB c =
let r,g,b = R c.R,G c.G,B c.B
max r g |> max b
+ ///returns the minimum value of the R, G, and B components of a color
let minRGB c =
let r,g,b = R c.R,G c.G,B c.B
min r g |> min b
- /// Creates a Color structure from the four ARGB component (alpha, red, green, and blue) values.
+ /// Creates a Color structure from the four ARGB components (alpha, red, green, and blue) values.
let fromArgb a r g b =
let f v =
if v < 0 || v > 255 then
@@ -99,7 +106,7 @@ module Colors =
byte v
{A= f a; R = f r; G = f g; B = f b}
- /// Creates a Color structure from the specified color values (red, green, and blue).
+ /// Creates a Color structure from the specified color component values (red, green, and blue).
/// The alpha value is implicitly 255 (fully opaque).
let fromRgb r g b =
fromArgb 255 r g b
@@ -107,7 +114,7 @@ module Colors =
// /// Gets the hue-saturation-brightness (HSB) brightness value for this Color structure.
// let getBrightness = ()
- /// Gets the hue-saturation-brightness (HSB) hue value, in degrees, for this Color structure.
+ /// Gets the hue component value of the hue-saturation-brightness (HSB) format, in degrees, for this Color structure.
let getHue c =
let min = minRGB c |> getValueFromCC
match maxRGB c with
@@ -117,7 +124,7 @@ module Colors =
| _ -> failwithf "" // can't be
- /// Gets the hue-saturation-brightness (HSB) saturation value for this Color structure.
+ /// Gets the saturation component value of the hue-saturation-brightness (HSB) format for this Color structure.
let getSaturation col =
let minimum = minRGB col
let maximum = maxRGB col
@@ -159,6 +166,7 @@ module Colors =
// http://graphicdesign.stackexchange.com/questions/3682/where-can-i-find-a-large-palette-set-of-contrasting-colors-for-coloring-many-d
+ ///Predefined colors
module Table =
let black = fromRgb 0 0 0
@@ -197,7 +205,64 @@ module Colors =
// From publication: Escaping RGBland: Selecting Colors for Statistical Graphics
// http://epub.wu.ac.at/1692/1/document.pdf
+ ///Scientifically proven well distinguishable colors (http://epub.wu.ac.at/1692/1/document.pdf)
module StatisticalGraphics24 =
- let a = 1
//
- //{2,63,165},{125,135,185},{190,193,212},{214,188,192},{187,119,132},{142,6,59},{74,111,227},{133,149,225},{181,187,227},{230,175,185},{224,123,145},{211,63,106},{17,198,56},{141,213,147},{198,222,199},{234,211,198},{240,185,141},{239,151,8},{15,207,192},{156,222,214},{213,234,231},{243,225,235},{246,196,225},{247,156,212}
+ let Blue1 = fromRgb 2 63 165
+ let Blue2 = fromRgb 125 135 185
+ let Blue3 = fromRgb 190 193 212
+ let Red1 = fromRgb 214 188 192
+ let Red2 = fromRgb 187 119 132
+ let Red3 = fromRgb 142 6 59
+ let LightBlue1 = fromRgb 74 111 227
+ let LightBlue2 = fromRgb 133 149 225
+ let LightBlue3 = fromRgb 181 187 227
+ let LightRed1 = fromRgb 230 175 185
+ let LightRed2 = fromRgb 224 123 145
+ let LightRed3 = fromRgb 211 63 106
+ let Green1 = fromRgb 17 198 56
+ let Green2 = fromRgb 141 213 147
+ let Green3 = fromRgb 198 222 199
+ let Orange1 = fromRgb 234 211 198
+ let Orange2 = fromRgb 240 185 141
+ let Orange3 = fromRgb 239 151 8
+ let Cyan1 = fromRgb 15 207 192
+ let Cyan2 = fromRgb 156 222 214
+ let Cyan3 = fromRgb 213 234 231
+ let Magenta1 = fromRgb 243 225 235
+ let Magenta2 = fromRgb 246 196 225
+ let Magenta3 = fromRgb 247 156 212
+
+ let private rand = new System.Random()
+
+ let private paletteArray =
+ [|
+ Blue1
+ Blue2
+ Blue3
+ Red1
+ Red2
+ Red3
+ LightBlue1
+ LightBlue2
+ LightBlue3
+ LightRed1
+ LightRed2
+ LightRed3
+ Green1
+ Green2
+ Green3
+ Orange1
+ Orange2
+ Orange3
+ Cyan1
+ Cyan2
+ Cyan3
+ Magenta1
+ Magenta2
+ Magenta3
+ |]
+
+ let getRandomColor() =
+ let index = rand.Next(0,23)
+ paletteArray.[index]
diff --git a/src/FSharpGephiStreamer/Either.fs b/src/FSharpGephiStreamer/Either.fs
index 4ff7f7e..1ca409e 100644
--- a/src/FSharpGephiStreamer/Either.fs
+++ b/src/FSharpGephiStreamer/Either.fs
@@ -1,7 +1,7 @@
namespace FSharpGephiStreamer
-// the two-track type
+/// Two-track return type for railway oriented programming
type Either<'TSuccess,'TFailure> =
| Success of 'TSuccess
| Failure of 'TFailure
@@ -9,56 +9,56 @@ type Either<'TSuccess,'TFailure> =
module Either =
- // convert a single value into a two-track result
+ /// convert a single value into a two-track result
let succeed x =
Success x
- // convert a single value into a two-track result
+ /// convert a single value into a two-track result
let fail x =
Failure x
- // apply either a success function or failure function
+ /// apply either a success function or failure function
let either successFunc failureFunc twoTrackInput =
match twoTrackInput with
| Success s -> successFunc s
| Failure f -> failureFunc f
- // convert a switch function into a two-track function
+ /// convert a switch function into a two-track function
let bind f =
either f fail
- // pipe a two-track value into a switch function
+ /// pipe a two-track value into a switch function
let (>>=) x f =
bind f x
- // compose two switches into another switch
+ /// compose two switches into another switch
let (>=>) s1 s2 =
s1 >> bind s2
- // convert a one-track function into a switch
+ /// convert a one-track function into a switch
let switch f =
f >> succeed
- // convert a one-track function into a two-track function
+ /// convert a one-track function into a two-track function
let map f =
either (f >> succeed) fail
- // convert a dead-end function into a one-track function
+ /// convert a dead-end function into a one-track function
let tee f x =
f x; x
- // convert a one-track function into a switch with exception handling
+ /// convert a one-track function into a switch with exception handling
let tryCatch f exnHandler x =
try
f x |> succeed
with
| ex -> exnHandler ex |> fail
- // convert two one-track functions into a two-track function
+ /// convert two one-track functions into a two-track function
let doubleMap successFunc failureFunc =
either (successFunc >> succeed) (failureFunc >> fail)
- // add two switches in parallel
+ /// add two switches in parallel
let plus addSuccess addFailure switch1 switch2 x =
match (switch1 x),(switch2 x) with
| Success s1,Success s2 -> Success (addSuccess s1 s2)
diff --git a/src/FSharpGephiStreamer/Grammar.fs b/src/FSharpGephiStreamer/Grammar.fs
index 8f0d579..012ab35 100644
--- a/src/FSharpGephiStreamer/Grammar.fs
+++ b/src/FSharpGephiStreamer/Grammar.fs
@@ -4,23 +4,28 @@
// https://github.com/graphstream/gs-gephi
+///Semantics and mappings to represent Gephi interpretable Attributes of Nodes and Edges
module Grammar =
+ ///Action performed on the Gephi graph
type Action =
| Add
| Change
| Delete
+ ///Node action performed on the Gephi graph
let formatNodeAction= function
| Add -> "an"
| Change -> "cn"
| Delete -> "dn"
+ ///Edge action performed on the Gephi graph
let formatEdgeAction= function
| Add -> "ae"
| Change -> "ce"
| Delete -> "de"
+ ///Direction of an edge
type EdgeDirection =
| Directed
| Undirected
@@ -32,6 +37,7 @@ module Grammar =
// TODO: LabelSize ? LabelColor ? LabelVisible
+ ///Common attributes of nodes and edges
type Attribute =
| Size of float
| Color of Colors.Color
@@ -49,7 +55,7 @@ module Grammar =
| UserDef of string * obj
-
+ ///converts an attribute to a JSON token
let attibuteToJsonProperty = function
| Size v -> JsonObject.newJprop "size" v
| Color v -> JsonObject.newJprop "color" (Colors.toWebColor v)
@@ -67,7 +73,7 @@ module Grammar =
| Attribute.UserDef (a,v) -> JsonObject.newJprop a v
- /// Returns json string for a node
+ /// Returns a properly formatted JSON string for a node
//{"an":{"1":{"label":"Test label","size": 50}}}
let jsonFormatNode (action:Action) nodeId (attributes:Attribute list) =
let jsonAttributes = attributes |> List.map attibuteToJsonProperty
@@ -81,7 +87,7 @@ module Grammar =
- /// Returns json string for an edge
+ /// Returns a properly formatted JSON string for an edge
//"""{"ae":{"2":{"source":0,"target":1,"directed":true}}}"""
let jsonFormatEdge (action:Action) edgeId sourceId targetId (attributes:Attribute list) =
let jsonAttributes =
diff --git a/src/FSharpGephiStreamer/JsonObject.fs b/src/FSharpGephiStreamer/JsonObject.fs
index c3242bd..5e9883e 100644
--- a/src/FSharpGephiStreamer/JsonObject.fs
+++ b/src/FSharpGephiStreamer/JsonObject.fs
@@ -1,5 +1,6 @@
namespace FSharpGephiStreamer
+///Helper functions to create and convert JSON objects/properties
module JsonObject =
open Newtonsoft.Json.Linq
diff --git a/src/FSharpGephiStreamer/RestFulAux.fs b/src/FSharpGephiStreamer/RestFulAux.fs
index 2ab304c..dd73f5a 100644
--- a/src/FSharpGephiStreamer/RestFulAux.fs
+++ b/src/FSharpGephiStreamer/RestFulAux.fs
@@ -1,7 +1,9 @@
namespace FSharpGephiStreamer
+///Helper functions for requests to the Streamer server on the Gephi side
module RestfulAux =
+ ///Represents error messages returned on error from the streamer server
type Error =
| Http_CreateRequestFailed of string
| Http_Response of int
@@ -12,27 +14,32 @@ module RestfulAux =
let private header = [ "content-type", "application/json"]
+ ///Generates an error-handled GET request
let generateGetRequest =
Either.tryCatch
(fun urlString -> Http.Request (urlString))
(fun exn -> Error.Http_CreateRequestFailed exn.Message)
+ ///Generates an error-handled POST request
let generatePostRequest urlString =
Either.tryCatch
(fun content -> Http.Request(urlString, headers = header, meth="POST", body = RequestBody.Text content))
(fun exn -> Error.Http_CreateRequestFailed exn.Message)
+ ///Generates an error-handled PUT request
let generatePutRequest urlString =
Either.tryCatch
(fun content -> Http.Request(urlString, headers = header, meth="PUT", body = RequestBody.Text content))
(fun exn -> Error.Http_CreateRequestFailed exn.Message)
+ ///Generates an error-handled DELETE request
let generateDelRequest =
Either.tryCatch
(fun urlString -> Http.Request(urlString, meth = "DELETE" ))
(fun exn -> Error.Http_CreateRequestFailed exn.Message)
+ ///Evaluates a http request to the streamer server. Handles errors without exceptions by returning the Error type instead of throwing an exception.
let evalHttpResponseText (response:HttpResponse) =
if response.StatusCode > 199 && response.StatusCode < 300 then
match response.Body with
diff --git a/src/FSharpGephiStreamer/Streamer.fs b/src/FSharpGephiStreamer/Streamer.fs
index 534c10c..b4dd143 100644
--- a/src/FSharpGephiStreamer/Streamer.fs
+++ b/src/FSharpGephiStreamer/Streamer.fs
@@ -12,13 +12,16 @@ module Streamer =
/// Converter type to map from a custom edge to a Grammar.Attribute list
type EdgeConverter<'edge> = 'edge -> Grammar.Attribute list
-
let mutable private envirmonmentURL = "http://localhost:8080/workspace1?operation=updateGraph"
+
+ ///change the url of the target streamer server (default:"http://localhost:8080/workspace1?operation=updateGraph")
let setEnvirmonment ip port workspace = envirmonmentURL <- sprintf "http://%s:%i/%s/?operation=updateGraph" ip port workspace
+
+ ///returns the url of the current target streamer server
let getEnvirmonment () = envirmonmentURL
- // Adds a node with NodeConverter
+ /// Adds a node to the gephi graph using the given node converters grammar attribute mapping
let addNode (nodeConverter:NodeConverter<'node>) nodeId =
let nodeId' = string nodeId
(Either.tryCatch
@@ -30,7 +33,7 @@ module Streamer =
(fun _ -> Success nodeId' )
(fun error -> Failure error )
- // Adds a node
+ /// Adds a node to the gephi graph given an id mapping (node -> nodeId)
let addNodeBy (f:'node -> string) =
(Either.tryCatch
(fun node -> (jsonFormatNode Action.Add (f node) [Grammar.Attribute.Size 1.0]))
@@ -41,7 +44,7 @@ module Streamer =
(fun s -> Success s )
(fun error -> Failure error )
- // Updates a node with NodeConverter
+ /// Updates a node on the gephi graph using the given node converters grammar attribute mapping
let updateNode (nodeConverter:NodeConverter<'node>) nodeId =
let nodeId' = string nodeId
(Either.tryCatch
@@ -54,7 +57,7 @@ module Streamer =
(fun error -> Failure error )
- // Removes a node by nodeId
+ /// Removes a node by nodeId
let removeNode nodeId =
let nodeId' = string nodeId
(Either.tryCatch
@@ -67,7 +70,7 @@ module Streamer =
(fun error -> Failure error )
- // Adds an edge
+ /// Adds an edge to the gephi graph using the given node converters grammar attribute mapping
let addEdge (edgeConverter:EdgeConverter<'edge>) edgeId sourceId targetId =
let edgeId', sourceId', targetId' = (string edgeId), (string sourceId), (string targetId)
(Either.tryCatch
@@ -79,7 +82,7 @@ module Streamer =
(fun _ -> Success edgeId' )
(fun error -> Failure error )
- // Adds an edge given a function that maps from edge to edgeId*sourceId*targetId
+ /// Adds an edge given a mapping from edge to (edgeId*sourceId*targetId)
let addEdgeBy (f:'edge -> string*string*string) =
(Either.tryCatch
@@ -94,7 +97,7 @@ module Streamer =
(fun error -> Failure error )
- /// Update edge (source and targe are immutable)
+ /// Update edge (source and target are immutable)
// (source and targe are not needed)
let updateEdge (edgeConverter:EdgeConverter<'edge>) edgeId sourceId targetId =
let edgeId', sourceId', targetId' = (string edgeId), (string sourceId), (string targetId)
@@ -108,7 +111,7 @@ module Streamer =
(fun error -> Failure error )
- // Removes an edge by edgeId
+ /// Removes an edge by edgeId
let removeEdge edgeId =
let edgeId'= string edgeId
(Either.tryCatch