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Has the GraphML standard been updated?

I downloaded the Rome database from the link.

enter image description here

The files in it are stored in the "GraphML" format. However, I am unable to import it into Mathematica or the YEd software. I would like to know what is happening and how to import them correctly. A similar unsolved issue can be found at the following link:

Import["D:/grafo113.28.graphml"]

Import::fmterr: Cannot import data as GraphML format.

Example (grafo113.28.graphml):

<?xml version="1.0" encoding="UTF-8"?>
<!-- This file was written by the internal XML-Handler of Y-Files.-->
<!DOCTYPE graphml SYSTEM "http://www.graphdrawing.org/dtds/graphml.dtd">
<graphml>
<graph edgedefault="undirected" id="G">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<node id="n3"/>
<node id="n4"/>
<node id="n5"/>
<node id="n6"/>
<node id="n7"/>
<node id="n8"/>
<node id="n9"/>
<node id="n10"/>
<node id="n11"/>
<node id="n12"/>
<node id="n13"/>
<node id="n14"/>
<node id="n15"/>
<node id="n16"/>
<node id="n17"/>
<node id="n18"/>
<node id="n19"/>
<node id="n20"/>
<node id="n21"/>
<node id="n22"/>
<node id="n23"/>
<node id="n24"/>
<node id="n25"/>
<node id="n26"/>
<node id="n27"/>
<edge id="e0" source="n1" target="n12"/>
<edge id="e1" source="n12" target="n2"/>
<edge id="e2" source="n12" target="n0"/>
<edge id="e3" source="n0" target="n14"/>
<edge id="e4" source="n14" target="n3"/>
<edge id="e5" source="n20" target="n8"/>
<edge id="e6" source="n3" target="n15"/>
<edge id="e7" source="n3" target="n16"/>
<edge id="e8" source="n16" target="n5"/>
<edge id="e9" source="n3" target="n17"/>
<edge id="e10" source="n3" target="n18"/>
<edge id="e11" source="n19" target="n7"/>
<edge id="e12" source="n7" target="n21"/>
<edge id="e13" source="n4" target="n15"/>
<edge id="e14" source="n21" target="n9"/>
<edge id="e15" source="n9" target="n13"/>
<edge id="e16" source="n9" target="n22"/>
<edge id="e17" source="n22" target="n11"/>
<edge id="e18" source="n23" target="n3"/>
<edge id="e19" source="n18" target="n7"/>
<edge id="e20" source="n18" target="n24"/>
<edge id="e21" source="n24" target="n6"/>
<edge id="e22" source="n25" target="n23"/>
<edge id="e23" source="n25" target="n24"/>
<edge id="e24" source="n25" target="n13"/>
<edge id="e25" source="n19" target="n16"/>
<edge id="e26" source="n25" target="n26"/>
<edge id="e27" source="n26" target="n10"/>
<edge id="e28" source="n27" target="n13"/>
<edge id="e29" source="n27" target="n8"/>
<edge id="e30" source="n7" target="n26"/>
</graph>
</graphml>


It looks like Syed is right. But I'm not sure what's behind the Import function. So now I don't understand why deleting that line <!DOCTYPE graphml SYSTEM "http://www.graphdrawing.org/dtds/graphml.dtd"> is OK.

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  • 3
    $\begingroup$ This seems to be an older file. Remove the <!DOCTYPE... line and try again. $\endgroup$
    – Syed
    Feb 23, 2023 at 14:53
  • $\begingroup$ Yes, indeed. I'm not sure why this line ` <!DOCTYPE... ` leads to destruction. I don't know exactly how this function works, right. $\endgroup$
    – licheng
    Feb 23, 2023 at 15:24
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    $\begingroup$ It fails with Import[..., "XML"] as well, unless specifying "ReadDTD" -> False. But that option cannot be used with Import[..., "GraphML"], so yes: find a way to remove that line. E.g., ImportString[ StringRiffle[ Select[StringSplit[Import[file, "String"], "\n"], Not@*StringStartsQ["<!DOCTYPE"]], "\n"], "GraphML" ] $\endgroup$
    – Szabolcs
    Feb 23, 2023 at 18:31

1 Answer 1

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Understanding the Problem

"GraphML" is an XML format. All these files start with

<?xml version="1.0" encoding="UTF-8"?>
<!-- This file was written by the internal XML-Handler of Y-Files.-->
<!DOCTYPE graphml SYSTEM "http://www.graphdrawing.org/dtds/graphml.dtd">
<graphml>

The "!DOCTYPE" declaration above contains a reference to a Document Type Definition (DTD) file. The purpose of a DTD is to define the structure and the legal elements and attributes of an XML document. An XML document validated against a DTD is both "Well Formed" and "Valid".

The URL for the Document Type Definition file "http://www.graphdrawing.org/dtds/graphml.dtd" is no longer valid, and needs to be replaced, or its reference deleted as mentioned by @Syed in the comments.

URLExecute["http://www.graphdrawing.org/dtds/graphml.dtd"]
(* Not Found  
The requested URL /dtds/graphml.dtd was not found on this server. *)

Solutions

@Szabolcs showed already how to delete the invalid line.

Here I Import one of the "rome/grafo1049.21.graphml" file as a "String", StringReplace the invalid URL with a valid URL for the "graphml.dtd" file, and then ImportString in the "GraphML" format.

ImportString[
    StringReplace[
        Import[
            "http://www.graphdrawing.org/download/rome-graphml.tgz"
            , {"TAR", "rome/grafo1049.21.graphml", "String"}
        ]
    , "http://www.graphdrawing.org/dtds/graphml.dtd" -> "http://graphml.graphdrawing.org/dtds/1.0rc/graphml.dtd"
    ]
    ,"GraphML"
]

enter image description here

You can replace the URL "http://www.graphdrawing.org/download/rome-graphml.tgz" with the local path to your downloaded file.

Comment

By the way, notice that you don't need to unpack your "rome-graphml.tgz" file to Import the files inside. Here I don't even download the whole file.

You can first just get the file names and then Import only the one you need directly, as shown above.

fileNameList = Import[
  "http://www.graphdrawing.org/download/rome-graphml.tgz"
  , {"TAR", "FileNames"}
];
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