Fix crashing `index` command when targeted directory contains subject files

[juhoinkinen]

The annif index command crashes when the targeted directory contains subject files (files with either *.tsv or *.key extensions):

annif index dummy-fi tests/corpora/archaeology/fulltext/
Traceback (most recent call last):
...
  File "/home/local/jmminkin/git/Annif/annif/corpus/subject.py", line 248, in from_string
    subject_ids.add(subject_index.by_uri(uri))
AttributeError: 'NoneType' object has no attribute 'by_uri'

The bug is due to this change done in PR #663.

I made the change because it seemed unnecessary and confusing to pass the subject index and language to DocumentDirectory when it is used only for obtaining documents to give suggestions to.

Reverting the change, i.e. passing subject index and language to DocumentDirectory is the simplest way to fix the bug, and on second thought maybe it also is better conceptually: corpora should have subject index and language defined, even if they are not used.

Also renames vars to better correspond their origin/usage: keyfile(name) -> subjfile(name).

[codecov[bot]]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (2d1d3ce) 99.66% compared to head (b602ea2) 99.66%.

Additional details and impacted files

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[san-uh]

Dear Annif colleagues, thank you for already working on this problem. We in the DNB have recently started using Annif 0.61.0 and have now noticed that we cannot currently use an "index" command with this version, so we have to switch back to 0.60.0. Just one question: Is a bugfix release 0.61.1 planned or will the solution come with 1.0? Thanks and greetings, Sandro

[juhoinkinen]

Hi @san-uh,

This bug realized only when the targeted directory contains files with either .tsv or .key extension (as far as I'm aware). Does index command work for you if you remove these files from the targeted directory (if there are them)?

[san-uh]

Hello @juhoinkinen, thank you very much for the explanation. I deleted the *.tsv files that were previously in the directory and the index command now works. So with this workaround annif 0.61.0 including index is usable. Thanks for the feedback! Sandro