1. Create backup

1. curl -X POST http://localhost:8080/fcrepo/rest/fcr:backup

2. You will be given a directory in message body.  For example: C:\Users\Dev\projects\dcs-package-ingest\package-ingest-integration\target\cargo\configurations\tomcat8x\temp\1496329063578-0

3. You will see one or more files named documents_N.bin.gz where N is a number like 000001 (e.g. documents_000001.bin.gz)

2. Unzip and inspect the documents_N.bin.gz files.  Look for modeshape node whose primaryType is ‘mode:namespaces’

1. `jq` is a great tool for inspecting very large json files.  To pretty-print so that tools like grep can be used, try , cat documents_00001.bin | jq .

1. Grep for ‘namespaces’.  You’ll see something like:

   Code Block

   { "metadata": { "id": "936198c317f1e7mode:namespaces" }, "content": { "key": "936198c317f1e7mode:namespaces", "parent": "936198c317f1e7jcr:system", "properties": { "http://www.jcp.org/jcr/1.0": { "primaryType": { "$name": "mode:namespaces" } } }, "children": [ { "key": "936198c317f1e7mode:namespaces-http://www.jcp.org/jcr/1.0", "name": "jcr" }, { "key": "936198c317f1e7mode:namespaces-http://www.jcp.org/jcr/nt/1.0", "name": "nt" }, { "key": "936198c317f1e7mode:namespaces-http://www.jcp.org/jcr/mix/1.0", "name": "mix" }, { "key": "936198c317f1e7mode:namespaces-http://www.w3.org/2004/02/skos/core#", "name": "skos" } }

   
   

The dump contains a json object whose primary type is “mode:namespaces”.  Nested within it is a “children” array that enumerates the namespaces known to modeshape.  It appears that Modeshape chooses a single random prefix on all internal identifiers.  Acknowledging that prefix, the modeshape namespaces enumeration follows a simple and obvious pattern.

When Fedora encounters a novel rdf namespace and prefix, it adds it to the map.  In many cases, the prefix is auto-generated, e.g. “ns001”.  So if Fedora encountered a SKOS term, at any point, it may contain a namespace entry like:

{
    "key": "936198c317f1e7mode:namespaces-http://www.w3.org/2004/02/skos/core#",
    "name": "ns004"
}

In Fedora 4.7.1 and 4.7.2, a new set of hard-coded namespaces were published in the internal .cnd file used by modeshape.  When started, any pre-existing namespaces that match the hard-coded namespaces, yet differ by prefix, are overwritten.  So the namespaces table may now contain an entry:

{          
    "key": "936198c317f1e7mode:namespaces-http://www.w3.org/2004/02/skos/core#",
    "name": "skos"
}

This overwriting of the namespaces table is problematic.  Objects that existed before the repository had been upgraded to 4.7.1 or 4.7.2 will still contain their _old_ namespace references, such as:

{
  "metadata": {
    "id": "936198c317f1e7/jcr:system/jcr:nodeTypes/{httpwww.w3.org200402skoscore#}Concept"
  },
  "content": {
    "key": "936198c317f1e7/jcr:system/jcr:nodeTypes/{httpwww.w3.org200402skoscore#}Concept",
    "parent": "936198c317f1e7jcr:nodeTypes",
    "properties": {
      "http://www.jcp.org/jcr/1.0": {
        "isQueryable": true,
        "primaryType": {
          "$name": "nt:nodeType"
        },
        "supertypes": [],
        "hasOrderableChildNodes": false,
        "isMixin": true,
        "isAbstract": false,
        "nodeTypeName": "ns004:Concept" << NOTE: THIS IS THE PROBLEMATIC LINE <<
      }
    }
  }

This inconsistency is at the root of the problem.

3. For each dangling namespace, add a new entry to the mode:namespaces node, for example:

    "children": [
      {
        "key": "936198c317f1e7mode:namespaces-http://www.jcp.org/jcr/1.0",
        "name": "jcr"
      },
      {
        "key": "936198c317f1e7mode:namespaces-http://www.jcp.org/jcr/nt/1.0",
        "name": "nt"
      },
      {
        "key": "936198c317f1e7mode:namespaces-http://www.jcp.org/jcr/mix/1.0",
        "name": "mix"
      },
      {
        "key": "936198c317f1e7mode:namespaces-http://www.w3.org/2004/02/skos/core#",
        "name": "skos"
      },
      {
        "key": "936198c317f1e7mode:namespaces-http://www.w3.org/2004/02/skos/core#",
        "name": "ns004"
      }
]

4. After the namespaces node has been fixed, gzip the file so that it retains its original name

5. Restore the backup via fcr:restore