diff --git a/app-rest-service/src/test/java/com/calpano/graphinout/apprestservice/AppRestServiceApplicationTests.java b/app-rest-service/src/test/java/com/calpano/graphinout/apprestservice/AppRestServiceApplicationTests.java index c3bda5c..70d1ad9 100644 --- a/app-rest-service/src/test/java/com/calpano/graphinout/apprestservice/AppRestServiceApplicationTests.java +++ b/app-rest-service/src/test/java/com/calpano/graphinout/apprestservice/AppRestServiceApplicationTests.java @@ -1,5 +1,6 @@ package com.calpano.graphinout.apprestservice; +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.springframework.beans.factory.annotation.Autowired; @@ -19,6 +20,7 @@ @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK, classes = AppRestServiceApplication.class) @AutoConfigureMockMvc @TestPropertySource(locations = "classpath:application-integrationtest.properties") +@Disabled("TODO impl") class AppRestServiceApplicationTests { @Autowired diff --git a/app-rest-service/src/test/java/com/calpano/graphinout/apprestservice/controller/GraphmlControllerTest.java b/app-rest-service/src/test/java/com/calpano/graphinout/apprestservice/controller/GraphmlControllerTest.java index 231cc82..48f891e 100644 --- a/app-rest-service/src/test/java/com/calpano/graphinout/apprestservice/controller/GraphmlControllerTest.java +++ b/app-rest-service/src/test/java/com/calpano/graphinout/apprestservice/controller/GraphmlControllerTest.java @@ -11,6 +11,8 @@ import com.calpano.graphinout.apprestservice.service.GraphmlReaderService; import java.io.File; import java.io.FileInputStream; + +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; @@ -21,6 +23,7 @@ import org.springframework.test.web.servlet.request.MockHttpServletRequestBuilder; @WebMvcTest(GraphmlController.class) +@Disabled("TODO impl") class GraphmlControllerTest { private static final File DATA_FILE = diff --git a/src/.DS_Store b/src/.DS_Store deleted file mode 100644 index 8c70e25..0000000 Binary files a/src/.DS_Store and /dev/null differ diff --git a/src/main/.DS_Store b/src/main/.DS_Store deleted file mode 100644 index 964ee28..0000000 Binary files a/src/main/.DS_Store and /dev/null differ diff --git a/src/main/doc/graph-ecosystem-datasets.ttl b/src/main/doc/graph-ecosystem-datasets.ttl deleted file mode 100644 index a0bd889..0000000 --- a/src/main/doc/graph-ecosystem-datasets.ttl +++ /dev/null @@ -1,189 +0,0 @@ -@prefix rdf: . -@prefix rdfs: . -@prefix dc: . -@prefix v: . -@prefix f: . -@prefix ds: . -# This syntax: https://www.w3.org/TR/turtle/ - -# -# -# -# == Datasets -# -ds:BioGRID - a v:Dataset ; - v:url ; - v:contains . - -ds:SnapDatasets - a v:Dataset ; - dc:title "Stanford Network Analysis Platform (SNAP)" ; - v:url ; - v:url ; - v:comment "since 2005; each graph is in a different format; normalized versions from https://sparse.tamu.edu/SNAP" -. - -ds:SuiteSparseMatrixCollection - a v:Dataset ; - v:url ; - v:comment "very large" ; - v:includes v:SnapDatasets -. -ds:MatrixMarket - a v:Dataset ; - v:url ; - v:writes f:MatrixMarketFormat ; - v:includes v:SuiteSparseMatrixCollection -. -ds:ARGVF - a v:Dataset ; - dc:title "MIVIA Graph Database ARG/VF" ; - v:url . - -ds:CASOS - a v:Dataset ; - dc:title "CASOS CMU CASOS Datasets" ; - v:url ; - v:writes f:GraphML . - -ds:ClueWeb09 - a v:Dataset ; - dc:title "ClueWeb09 Web Graph" ; - v:writes f:TGF ; - v:url ; - v:related -. - -ds:DIMACS10 - a v:Dataset ; - dc:title "DIMACS10 [113] DIMACS Implementation Challenges DIMACS" ; - v:writes f:DimacsFormat . - -ds:DSI - a v:Dataset ; - dc:title "DSI [114], [115] Web Algorithmics Lab Data" ; - v:url ; - dc:subject "web crawl" . - -ds:KaggleDatasets - a v:Dataset ; - v:url ; - v:contains ; - v:comment "1800 network datasets; each in a different format" ; - v:writes f:CustomCsv -. - -ds:Netzschleuder - a v:Dataset ; - v:url ; - v:comment "280 graphs" ; - v:writes ( f:GraphML f:GML f:CustomCsv ) -. - -ds:LodCloud - a v:Dataset ; - v:url ; - v:comment "1,255 datasets" . - -ds:GraphBench - a v:Dataset ; - dc:title "GraphBench [119] GraphBench" ; - v:writes f:TGF ; - v:url . - -ds:HOG - a v:Dataset ; - dc:title "HOG [120] The House of Graphs" ; - v:writes f:TGF ; - v:url . - -ds:WebDataCommonsHyperlink - a v:Dataset ; - dc:title "Hyperlink [122] Web Data Commons - Hyperlink; Graphs Pajek, WebGraph" ; - v:url ; - v:writes f:PajekFormat . - -ds:IamGraph - a v:Dataset ; - dc:title "IAM [123] IAM Graph Database Repository" ; - v:writes f:GXL ; - v:url . - -ds:PajekDatasets - a v:Dataset ; - v:url ; - v:writes f:PajekFormat ; - v:comment "ca. 30 graphs" . - -ds:SGB - a v:Dataset ; - dc:title "SGB [77], [126] Stanford GraphBase SGB" ; - v:comment "10 graphs from Donal Knuth" ; - v:url . - - - a v:Dataset ; - v:comment "15 networks" . - -ds:InternetTopologyZoo - a v:Dataset ; - dc:title "Zoo [105] Internet Topology Zoo" ; - v:writes f:GraphML ; - v:url . - -ds:HPRD - a v:Dataset ; - dc:title "Human Protein Reference Database" ; - v:url ; - v:writes f:PsiMiTab25 . - -ds:NetworkRepository - a v:Dataset ; - v:url ; - v:comment "1000+ graphs" ; - v:writes f:MatrixMarketFormat -. - -# -# -# -# == Famous Graphs/Datasources -ds:Enron - a v:Datasource ; - v:doc ; - v:url -# TSV - ; - v:url ; - v:url -. - -ds:NVD - a v:Datasource ; - v:url ; - dc:title "National Vulnerability Database" ; - v:url ; - # import in Neo4j - v:url . - - -ds:MavenCentralDependencies - a v:Dataset ; - v:url ; - v:url . - -ds:OffshoreLeaks - a v:Datasource ; - v:url ; - v:comment "includes Panama Papers" . - - -ds:W3cDumps - a v:Dataset ; - v:url ; - v:comment "2014, ca. 30 larger kgraphs" . - - -# TODO wikidata -# TODO smw diff --git a/src/main/doc/graph-ecosystem-formats.ttl b/src/main/doc/graph-ecosystem-formats.ttl deleted file mode 100644 index 882baf6..0000000 --- a/src/main/doc/graph-ecosystem-formats.ttl +++ /dev/null @@ -1,304 +0,0 @@ -@base . -@prefix rdf: . -@prefix rdfs: . -@prefix dc: . -@prefix v: <./graph-ecosystem-vocab.ttl#> . -@prefix v: . -@prefix f: . -# This syntax: https://www.w3.org/TR/turtle/ -# -# -# == Format -f:Gram - a v:Format ; - v:url ; - v:comment "invented by neo4j" ; - v:related v:Neo4j -. - -f:CustomCsv - a v:TextFormat ; - v:comment "often nodes file and edges file are used in some ad-hoc format" -. - -f:DimacsFormat - a v:Format ; - v:related v:DIMACS10 ; - dc:title "DIMACS Graph Format" ; - v:spec -. -# weird format, lots of different files -f:JsonGraph - a v:JsonFormat ; - v:url ; - v:comment "seems relevant" -. - -f:TGF - a v:Format ; - dc:title "Trivial Graph Format" ; - v:url -. - -f:GEXF - a v:Format ; - dc:title "Graph Exchange XML Format" ; - v:spec ; - v:examples -. - -f:GML - a v:Format ; - dc:title "Graph Modelling Language" ; - v:url ; - v:spec ; - v:spec ; - v:url ; - v:fileExt ".gml" ; - v:comment "predecessor of GraphML" -. - -f:GraphML - a v:XmlFormat ; - v:comment "since 2000" ; - v:wikipedia "https://en.wikipedia.org/wiki/GraphML" ; - dc:title "Graph Markup Language" ; - v:spec ; - v:examples -. - -f:RDF_NTriples - a v:Format ; - dc:title "RDF in N-Triples format" -. - -f:LEDA - a v:TextFormat ; - v:comment "today irrelevant, homepage last updated in 2006" ; - v:spec -. - -f:PajekFormat - a v:TextFormat ; - dc:title "Pajekt NET format" ; - v:spec ; - v:url ; - v:fileExt ( ".net" ".paj" ) -. - -f:GXL - a v:XmlFormat ; - dc:title "Graph eXchange Language" ; - v:comment "homepage from 2002" ; - v:url ; - v:url -. - -f:SparseGraph6 - a v:Format ; - v:comment "looks irrelevant" ; - v:spec -. - -f:BioGridTab3 - a v:Format ; - dc:title "BioGRID Tab 3.0 Format" ; - v:comment "ca. 1 Mio edges in total in the database" ; - v:fileExt ( ".tab3.txt" ".tab3.zip" ) ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:spec -. - -f:PsiMiTab25 - a v:TextFormat ; - v:comment "Protenomics Standards Initiative Molecular Interaction; since 2002" ; - v:spec ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - dc:title "PSI-MI Tab Version 2.5 Format" -. - -f:PsiMiXml25 - a v:XmlFormat ; - v:comment "Protenomics Standards Initiative Molecular Interaction; since 2002" ; - v:spec ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - dc:title "PSI-MI XML Version 2.5 Format" -. - -f:bintsv4 - a v:BinaryFormat ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "deprecated; since 2009; internal format of discontinued GraphLab/PowerGraph tool?" -. - -f:DOT - a v:TextFormat ; - v:wikipedia ; - v:spec ; - v:comment "GraphVis Dot Language; since 2000" ; - dc:title "DOT (graphviz syntax)" ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:fileExt ( ".dot" ".gv" ) -. - -f:PerlGraphEasyFormat - a v:TextFormat ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "Perl Graph::Easy format; since 2004; LOOKS IRRELEVANT TODAY" -. - - -f:ITDK - a ( v:Format v:Dataset ) ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "[41] X CAIDA Internet Topology Data Kit; since 2002; very specific format (node file & edge file)" -. - - -f:JsonGraph - a v:JsonFormat ; - v:spec ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "since 2014" -. - - -f:TEI - a v:Format ; - dc:title "Text Encoding Initiative Graph Format (XML-compatible)" ; - v:comment "IRRELEVANT; since 2001" ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:spec -. - -f:YGF - a v:BinaryFormat ; - v:spec ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "DEPRECATED yWorks/yEd Graph Format; since 2004" -. - - -f:Netdraw - a v:TextFormat ; - dc:title "Netdraw VNA format" ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "irrelevant" -. - -f:UCINET - a v:TextFormat ; - dc:title "UCINET DL Format" ; - v:spec ; - v:comment "Unfortunately, a reference page or manual seems not to be available about UCINET file formats." -. - -f:GUESS - a v:TextFormat ; - dc:title "GUESS format (GDF)" ; - v:comment "irrelevant" ; - v:spec ; - v:url -. - -f:NNF - a v:Format ; - v:fileExt ".nnf" ; - dc:title "Nested Network Format" ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "[59], [60] ; since 2003" -. - -f:SIF - a v:TextFormat ; - v:comment "since 2003" ; - dc:title "Simple Interaction Format" ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:fileExt ".sif" ; - v:spec -. - - - -f:XGMML - a v:XmlFormat ; - v:related v:GML ; - v:wikipedia ; - v:comment "based on GML; " -. - -f:SBML - a v:XmlFormat ; - dc:title "Systems Biology Markup Language (SBML)" ; - v:claim "format to describe biochemical networks" ; - v:spec -. - -f:BioPAX - a v:OwlFormat ; - dc:title "BioPAX (Biological PAthways eXchange) Format" ; - v:claim "designed to exchange biological pathways data" ; - v:spec -. - -f:CytoscapeJsonFormat - a v:Format ; - v:comment "export Cytoscape graphs to the browser" ; - v:spec ; - v:related v:CytoscapeCX -. - -f:CytoscapeCX - a v:Format ; - v:spec ; - v:spec ; - v:comment "seems active and relevant" -. - -f:OGDL - a v:TextFormat ; - v:spec ; - dc:title "Ordered Graph Data Language" ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "since 2002; seems mostly to be used as config files; see also Apache Shiro" -. - -f:LGF - a v:TextFormat ; - dc:title "LEMON Graph Format" ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "since 2008" ; - v:spec -. - -f:OGML - a v:Format ; - dc:title "Open Graph Markup Language" ; - v:coveredIn v:PaperGraphExchangeFileFormats ; - v:comment "seems to be proposed in 1 paper and forgotten since; since 2012" ; - v:url -. - -f:MATLAB - a v:Format ; - v:fileExt ".mat" -. - -f:RutherfordBoeing - a v:Format ; - v:comment "looks irrelevant" ; - v:comment "for FORTRAN" -. - -f:MatrixMarketFormat - a v:Format ; - v:comment "the native format of Matrix Market; seems relevant" ; - v:fileExt ".mtx" ; - v:url ; - v:spec -. - -f:GDL - a v:TextFormat ; - dc:title "Graph Drawing Language" ; - v:comment "used by Perl:Easy" . diff --git a/src/main/doc/graph-ecosystem-vocab.ttl b/src/main/doc/graph-ecosystem-vocab.ttl deleted file mode 100644 index 0aba048..0000000 --- a/src/main/doc/graph-ecosystem-vocab.ttl +++ /dev/null @@ -1,119 +0,0 @@ - # -# This syntax: https://www.w3.org/TR/turtle/ -# -@prefix rdf: . -@prefix rdfs: . -@prefix dc: . -@prefix v: . -# == Vocabulary -v:Paper - a rdfs:Class . - -v:GraphResource - a rdfs:Class . - -v:Datasource - rdfs:subClassOf v:GraphResource ; - v:comment "A datasource can be converted to a graph or multiple graphs" ; - a rdfs:Class . - -v:Dataset - rdfs:subClassOf v:GraphResource ; - a rdfs:Class . - -v:App - rdfs:subClassOf v:GraphResource ; - a rdfs:Class . - -v:Format - rdfs:subClassOf v:GraphResource ; - a rdfs:Class . - -v:BinaryFormat - a rdfs:Class ; - rdfs:subClassOf v:Format . - -v:TextFormat - a rdfs:Class ; - rdfs:subClassOf v:Format . - -v:TripleFormat - a rdfs:Class ; - v:comment "maybe convert using https://github.com/architolk/rdf2graphml" ; - rdfs:subClassOf v:Format . - -v:XmlFormat - a rdfs:Class ; - rdfs:subClassOf v:TextFormat . - -v:OwlFormat - a rdfs:Class ; - rdfs:subClassOf v:TripleFormat . - -v:JsonFormat - a rdfs:Class ; - rdfs:subClassOf v:TextFormat . - -v:claim - a rdf:Property ; - rdfs:domain rdf:value . - -v:related - a rdf:Property ; - rdfs:domain rdfs:Resource . - -v:includes - a rdf:Property ; - v:comment "one dataset my include another one" ; - rdfs:range v:Dataset ; - rdfs:domain v:Dataset . - -v:examples - a rdf:Property ; - rdfs:domain rdfs:Resource . - -v:fileExt - a rdf:Property ; - rdfs:domain rdf:value . - -v:comment - a rdf:Property ; - rdfs:domain rdf:value . - - -v:license - a rdf:Property . - -v:spec - a rdf:Property . - -v:language - a rdf:Property . - -v:url - a rdf:Property . - -v:wikipedia - a rdf:Property . - -v:reads - a rdf:Property ; - rdfs:domain v:Format . - -v:writes - a rdf:Property ; - rdfs:domain v:Format . - -v:coveredIn - a rdf:Property ; - rdfs:domain v:GraphResource ; - rdfs:range v:Paper -. - -v:contains - a rdf:Property ; - rdfs:domain v:Dataset . - -v:doc - a rdf:Property ; - v:comment "documentation URL" . \ No newline at end of file diff --git a/src/main/doc/graph-ecosystem.ttl b/src/main/doc/graph-ecosystem.ttl deleted file mode 100644 index f97ba98..0000000 --- a/src/main/doc/graph-ecosystem.ttl +++ /dev/null @@ -1,199 +0,0 @@ -@prefix rdf: . -@prefix rdfs: . -@prefix dc: . -@base . -@prefix v: . -@prefix f: . -@prefix ds: . -# This syntax: https://www.w3.org/TR/turtle/ - -# -# -# == Research -v:PaperGraphExchangeFileFormats - a v:Paper ; - v:url ; - dc:title "Unravelling Graph-Exchange File Formats" ; - dc:creator ( "Matthew Roughan" "Jonathan Tuke" ) ; - dc:date "2015" ; - v:comment "A great paper on graph file formats including links to graph data repositories -- time frames indicate when the format was/is used" -. - -# -# -# -# -# -# == Apps -# - - a v:App ; - dc:title "KrackPlot" ; - v:comment "OLD" . - - - a v:App ; - v:comment "academic" ; - v:claim "LEMON stands for Library for Efficient Modeling and Optimization in Networks. It is a C++ template library providing efficient implementations of common data structures and algorithms with focus on combinatorial optimization tasks connected mainly with graphs and networks." . - -<#Maven> - a v:App ; - v:writes ( f:DOT f:GraphML ) ; - v:url ; - v:comment "'mvn dependency:tree -DoutputType=graphml' (or 'dot')" -. - -<#PajekApp> - a v:App ; - v:claim "Analysis and visualization of very large networks" ; - v:license "" ; - v:reads f:PajekFormat ; - v:url . - - - a v:App ; - v:reads f:Netdraw . - - - a v:App ; - v:reads f:GUESS ; - v:comment "last update in 2007" ; - v:claim "GUESS is an exploratory data analysis and visualization tool for graphs and networks. " ; - v:license "GPL" -. - - - a v:App ; - v:language "js" ; - v:license ( "MIT" "Apache" ) ; - v:reads "custom JS" . - -<#NetworkX> - a v:App ; - v:license "BSD" ; - v:language "Python" ; - v:claim "Visualization is not a focus on NetworkX, but it is a major feature for many users. We need to enhance the drawing tools for NetworkX." ; - v:related ( f:MatrixMarketFormat f:GEXF f:GML f:GraphML f:LEDA f:SparseGraph6 f:PajekFormat ) ; - v:url . - -<#Gephi> - a v:App ; - dc:title "Gephi" ; - v:claim "The Open Graph Viz Platform" ; - v:license "GPL" ; - v:url ; - v:reads f:DOT . - - -<#Cytoscape> - a v:App ; - v:claim "" ; - v:license "" ; - v:url ; - v:comment "yWorks has a plugin for it" ; ; - v:reads ( f:SIF f:NNF f:GML f:XGMML f:SBML f:BioPAX f:GraphML f:CytoscapeJsonFormat ) -. - -<#Graph-tool> - a v:App ; - v:claim "Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs" ; - v:license "" ; - v:language "Python" ; - v:url . - -<#Graphviz> - a v:App ; - v:claim "" ; - v:license "" ; - v:url ; - v:reads f:DOT . - -<#Tulip> - a v:App ; - dc:title "Tulip TLP format" ; - v:claim "Tulip is an open source, cross-platform, data visualization framework mainly dedicated to the analysis, the drawing and the visualization of very large graphs (up to the million of nodes and edges)." ; - v:license "GPL" ; - v:url . - -<#yEd> - a v:App ; - v:claim "" ; - v:license "commercial/free" ; - v:url ; - v:reads ( f:GraphML ) ; - v:related <#Graphity> . - -<#yEdLive> - a v:App ; - v:url -. - -<#SnapTool> - a v:App ; - v:url ; - v:claim - "Stanford Network Analysis Platform (SNAP) is a general purpose, high performance system for analysis and manipulation of large networks." -. - -<#Graphity> - a v:App ; - v:claim "The diagram editor with automatic layouts" ; - v:url . - -<#AllegroGraph> - a v:App ; - v:claim "Entity Event Knowledge Graphs" ; - v:license "commercial" ; - v:url ; - v:related <#Gruff> -. - -<#Gruff> - a v:App ; - v:url "https://allegrograph.com/products/gruff/" ; - v:claim - "The Industry's most advanced no-code Graph Visualization, Graphical Query Builder, and Knowledge Graph Explorer" . - -<#NetworkX> - a v:App ; - v:claim "NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks." ; - v:license "" ; - v:url . - -<#NodeXL> - a v:App ; - v:claim "Twitter analysis in Power BI" ; - v:license "" ; - v:url . - -<#NetMiner> - a v:App ; - v:claim "Since 2001, world's best, general-purpose, all-in-one Network Analysis software" ; - v:license "commercial" ; - v:url . - -<#:PerlGraphEasy> - a v:App ; - v:url ; - v:url ; - v:writes ( f:GraphML f:DOT f:GDL ) ; - v:reads f:PerlGraphEasyFormat . - -<#GraphTool> - a v:App ; - dc:title "Graph-tool" ; - v:claim "efficient network analysis" ; - v:url ; - v:url ; - v:language "Python" ; - v:comment "modern, powerful" -. -# -# -# - -# == TODO -v:Neo4j - a v:App . -# Jupyter -- yWorks -# neo4j -- yWorks