fix the problem of trying to get edges which are not in the graph when running pra

[IdelCoder]

1. The change on code is only in PathFinder.scala. The other twos change nothing.
2. To run pra, some spec_files need to change. The changes for me just runs OK.

[matt-gardner]

Thanks for the PR! I'm confused about some of the config file changes, though - I'm concerned you're actually changing behavior by removing some of them.

[matt-gardner]

This should go in your global .gitignore file, not here. So should most of the other entries here, but I made this before learning better practices...

[matt-gardner]

Are you sure removing all of these parameters is correct, here?

[matt-gardner]

Can you remove your machine-specific path, here? Something like /embedding_dir/pca_svo/embeddings.tsv would be better - it's more obvious that a user is intended to change the path this way. Also, the code used to not require you to give a full path... Not sure if you can just use "pca_svo" here any more or not. It's been quite a while since I touched this code.

[matt-gardner]

There's a slightly more idiomatic way to do this in scala, using flatMap instead of a filter:

fileUtil.readLinesFromFile(embeddingsFile).flatMap(line => {
  val fields = line.split("\t");
  if (graph.hasEdge(fields(0))) {
    val relationIndex = graph.getEdgeIndex(fields(0))
    val vector = fields.drop(1).map(_.toDouble)
    Seq((relationIndex, new Vector(vector)))
  } else {
    Seq()
  }
}.toMap

This saves a tiny bit of memory and processing time, also, as you're not constructing vectors unless the edge is in the graph.

[matt-gardner]

This added import is unused - I think you can just revert all of the changes to this file.

[IdelCoder]

Sorry for late reply and my poor programming. I once tried to alter the path of "embeddings" to be relative. So I tried to made some change on the code but failed.