From b79cd88f440fcb80cc5e3d84a7b8df6c5ac9a160 Mon Sep 17 00:00:00 2001 From: fchrstou Date: Sat, 31 Aug 2024 10:44:44 +0200 Subject: [PATCH] MInor changes --- src/metagraphml.jl | 22 ++- test/Manifest.toml | 147 +++++++------- test/metagraphsio.jl | 6 +- test/runtests.jl | 4 +- test/testdata/ITZ_Aarnet.graphml | 317 +++++++++++++++++++++++++++++++ test/testdata/ITZ_Sprint.graphml | 266 ++++++++++++++++++++++++++ 6 files changed, 686 insertions(+), 76 deletions(-) create mode 100644 test/testdata/ITZ_Aarnet.graphml create mode 100644 test/testdata/ITZ_Sprint.graphml diff --git a/src/metagraphml.jl b/src/metagraphml.jl index 2b3ae7f..4ef003c 100644 --- a/src/metagraphml.jl +++ b/src/metagraphml.jl @@ -63,17 +63,19 @@ function _get_key_props(doc::EzXML.Document) keynodes = findall("//x:key", doc.root, ["x"=>ns]) keyprops = Dict{String,AttrKey}() for keynode in keynodes - attrtype = graphMLAttributesType[strip(keynode["attr.type"])] - keyadded = false - for childnode in EzXML.eachnode(keynode) - if EzXML.nodename(childnode) == "default" - defaultcontent = strip(nodecontent(childnode)) - keyprops[keynode["id"]] = AttrKey(keynode["id"], keynode["attr.name"], graphlMLAttributesDomain[keynode["for"]], attrtype, attrtype == String ? defaultcontent : parse(attrtype, defaultcontent) ) - keyadded = true + if any(x -> nodename(x)=="attr.type",attributes(keynode)) + attrtype = graphMLAttributesType[strip(keynode["attr.type"])] + keyadded = false + for childnode in EzXML.eachnode(keynode) + if EzXML.nodename(childnode) == "default" + defaultcontent = strip(nodecontent(childnode)) + keyprops[keynode["id"]] = AttrKey(keynode["id"], keynode["attr.name"], graphlMLAttributesDomain[keynode["for"]], attrtype, attrtype == String ? defaultcontent : parse(attrtype, defaultcontent) ) + keyadded = true + end + end + if !keyadded + keyprops[keynode["id"]] = AttrKey(keynode["id"], keynode["attr.name"], graphlMLAttributesDomain[keynode["for"]], attrtype, nothing ) end - end - if !keyadded - keyprops[keynode["id"]] = AttrKey(keynode["id"], keynode["attr.name"], graphlMLAttributesDomain[keynode["for"]], attrtype, nothing ) end end return keyprops diff --git a/test/Manifest.toml b/test/Manifest.toml index 4a41976..567ed62 100644 --- a/test/Manifest.toml +++ b/test/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.9.1" +julia_version = "1.10.4" manifest_format = "2.0" project_hash = "fd4b68bfd9948c52096ec5fe8b1aea5986f0fb1d" [[deps.AbstractTrees]] -git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.4" +version = "0.4.5" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -15,9 +15,9 @@ version = "1.1.1" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] -git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" +git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" -version = "0.2.0" +version = "0.4.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -26,10 +26,10 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.Compat]] -deps = ["UUIDs"] -git-tree-sha1 = "4e88377ae7ebeaf29a047aa1ee40826e0b708a5d" +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.7.0" +version = "4.15.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -38,13 +38,13 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.2+0" +version = "1.1.1+0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "cf25ccb972fec4e4817764d01c82386ae94f77b4" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.14" +version = "0.18.20" [[deps.Dates]] deps = ["Printf"] @@ -78,15 +78,15 @@ version = "1.6.0" [[deps.EzXML]] deps = ["Printf", "XML2_jll"] -git-tree-sha1 = "0fa3b52a04a4e210aeb1626def9c90df3ae65268" +git-tree-sha1 = "380053d61bb9064d6aa4a9777413b40429c79901" uuid = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615" -version = "1.1.0" +version = "1.2.0" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" +git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.1" +version = "1.16.3" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -111,58 +111,63 @@ version = "0.7.0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" +git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.8.0" +version = "1.11.2" [[deps.Inflate]] -git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" +git-tree-sha1 = "d1b1b796e47d94588b3757fe84fbf65a5ec4a80d" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.3" +version = "0.1.5" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "PrecompileTools", "Reexport", "Requires", "TranscodingStreams", "UUIDs", "Unicode"] +git-tree-sha1 = "5fe858cb863e211c6dedc8cce2dc0752d4ab6e2b" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.31" +version = "0.4.50" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" -version = "0.6.3" +version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "7.84.0+0" +version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -version = "1.10.2+0" +version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -173,9 +178,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.13" [[deps.Markdown]] deps = ["Base64"] @@ -184,7 +189,7 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+0" +version = "2.28.2+1" [[deps.MetaGraphs]] deps = ["Graphs", "JLD2", "Random"] @@ -197,7 +202,7 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.10.11" +version = "2023.1.10" [[deps.NestedGraphs]] deps = ["AbstractTrees", "DocStringExtensions", "Graphs", "SimpleTraits"] @@ -226,23 +231,29 @@ version = "1.2.0" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.21+4" +version = "0.3.23+4" [[deps.OrderedCollections]] -git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282" +git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.0" +version = "1.6.3" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.9.0" +version = "1.10.0" + +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" +git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.0" +version = "1.4.3" [[deps.Printf]] deps = ["Unicode"] @@ -253,7 +264,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[deps.Random]] -deps = ["SHA", "Serialization"] +deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Reexport]] @@ -290,31 +301,36 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "0da7e6b70d1bb40b1ace3b576da9ea2992f76318" +deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] +git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.0" -weakdeps = ["Statistics"] +version = "1.9.7" [deps.StaticArrays.extensions] + StaticArraysChainRulesCoreExt = "ChainRulesCore" StaticArraysStatisticsExt = "Statistics" + [deps.StaticArrays.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + [[deps.StaticArraysCore]] -git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.0" +version = "1.4.3" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.9.0" +version = "1.10.0" [[deps.SuiteSparse_jll]] -deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "5.10.1+6" +version = "7.2.1+1" [[deps.TOML]] deps = ["Dates"] @@ -332,15 +348,18 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TestSetExtensions]] deps = ["DeepDiffs", "Distributed", "Test"] -git-tree-sha1 = "3a2919a78b04c29a1a57b05e1618e473162b15d0" +git-tree-sha1 = "ccebd99935be339d2ad907589708ba1f0d62bab3" uuid = "98d24dd4-01ad-11ea-1b02-c9a08f80db04" -version = "2.0.0" +version = "3.0.0" [[deps.TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" +git-tree-sha1 = "96612ac5365777520c3c5396314c8cf7408f436a" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.13" +version = "0.11.1" +weakdeps = ["Random", "Test"] + + [deps.TranscodingStreams.extensions] + TestExt = ["Test", "Random"] [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -350,27 +369,27 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] +git-tree-sha1 = "d9717ce3518dc68a99e6b96300813760d887a01d" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.10.3+0" +version = "2.13.1+0" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" +version = "1.2.13+1" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+0" +version = "5.8.0+1" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" diff --git a/test/metagraphsio.jl b/test/metagraphsio.jl index b2fd25d..3719c2f 100644 --- a/test/metagraphsio.jl +++ b/test/metagraphsio.jl @@ -36,5 +36,9 @@ end rm(ftname) - # Write your tests here. + # ITZ graphml + ftname = joinpath(testdir, "testdata", "ITZ_Aarnet.graphml") + dmg2 = open(ftname, "r") do io + loadgraphs(io, GraphMLFormat(), MGFormat()) + end end diff --git a/test/runtests.jl b/test/runtests.jl index 578ca99..3cecf3c 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -14,5 +14,7 @@ testdir = dirname(@__FILE__) include("testutils.jl") @testset "NestedGraphsIO.jl" begin - @includetests ["metagraphsio", "nestedgraphsio"] + foreach(["metagraphsio.jl", "nestedgraphsio.jl"]) do x + include(x) + end end diff --git a/test/testdata/ITZ_Aarnet.graphml b/test/testdata/ITZ_Aarnet.graphml new file mode 100644 index 0000000..eae22a3 --- /dev/null +++ b/test/testdata/ITZ_Aarnet.graphml @@ -0,0 +1,317 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2/12/10 + Australia + Country + AARNET + Primary + 0 + http://www.aarnet.edu.au/aarnet3.aspx + 1.0 + REN + Current + 1 + 0 + Aarnet + 0.3.34dev-20120328 + 0 + 0 + e278b1b + = + 08 + 3/08/10 + IP + Topology Zoo Toolset + 1 + 0 + 2010_08 + 2010 + 2011_09_01 + 0 + + 1 + -33.86785 + Australia + 0 + 151.20732 + Sydney1 + + + 1 + -27.46794 + Australia + 1 + 153.02809 + Brisbane2 + + + 1 + -35.28346 + Australia + 2 + 149.12807 + Canberra1 + + + 1 + -33.86785 + Australia 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