bug in maintenance add-species introduced in #1646

[AprilYUZhang]

Hi guys, currently I am building pig's demorgraphy. when I run python -m maintenance add-species sus_scrofa , there is a bug happend, here is the error report:

 2025-01-23 19:20:06,515 [17802] INFO     maint: Adding new species SusScr for Ensembl ID sus_scrofa
2025-01-23 19:20:06,516 [17802] INFO     ensembl: making request to http://rest.ensembl.org/info/assembly/sus_scrofa?synonyms=1
2025-01-23 19:20:10,560 [17802] INFO     ensembl: making request to http://rest.ensembl.org/info/data
2025-01-23 19:20:10,758 [17802] INFO     maint: Writing genome data for SusScr sus_scrofa
2025-01-23 19:20:10,826 [17802] INFO     ensembl: making request to http://rest.ensembl.org/info/genomes/sus_scrofa
2025-01-23 19:20:11,161 [17802] INFO     maint: SusScr: name=Sus scrofa, common_name=Pig
2025-01-23 19:20:11,164 [17802] CRITICAL root: Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/Users/*/Experinment/git_repository/stdpopsim/maintenance/__main__.py", line 6, in <module>
    main.main()
  File "/Users/*/Experinment/git_repository/stdpopsim/maintenance/main.py", line 544, in main
    cli()
  File "/Users/*/opt/anaconda3/envs/stdpopsim_env/lib/python3.12/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/*/opt/anaconda3/envs/stdpopsim_env/lib/python3.12/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/Users/*/opt/anaconda3/envs/stdpopsim_env/lib/python3.12/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/*/opt/anaconda3/envs/stdpopsim_env/lib/python3.12/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/*/opt/anaconda3/envs/stdpopsim_env/lib/python3.12/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/*/Experinment/git_repository/stdpopsim/maintenance/main.py", line 515, in add_species
    writer.add_species(ensembl_id.lower(), force=force)
  File "/Users/*/Experinment/git_repository/stdpopsim/maintenance/main.py", line 276, in add_species
    write_catalog_stub(
  File "/Users/*/Experinment/git_repository/stdpopsim/maintenance/main.py", line 225, in write_catalog_stub
    chr_names = genome_data["chromosomes"].keys()
                ~~~~~~~~~~~^^^^^^^^^^^^^^^
TypeError: tuple indices must be integers or slices, not str

I guess it might be caused by recent modification, because I didn't receive this error message last week running the same command. Does anyone know why it's giving an error？ Thank you very much!

[petrelharp]

Hm, thanks for the report. Just checking - what version of stdpopsim are you using? Is it pip install'ed, or from github? If not from github, could you grab that and try again?

[AprilYUZhang]

Hi,thank you for your reply! I clone the fork from GitHub. Here is the latest commit in my branch.

commit cb1550ab1a59f90e5034c597eceab9de4555945d (HEAD -> sus_scrofa, origin/main, origin/HEAD, main)
Author: Clara Rehmann <[email protected]>
Date:   Wed Jan 22 20:56:00 2025 -0800

    Dromel qc (#1668)
    
    * qc for DroMel DFE

[petrelharp]

I can confirm this, and reverting to just before @andrewkern's #1646 fixes the problem.

If I insert print(genome_data) just before the line in question, I see that it is

('updated', None)

which is why we get an error trying to look at genome_data["chromosomes"].

I'm guessing this will be easy to fix when @andrewkern has a minute to look at it.

[andrewkern]

darn! this was broken in the changes I introduced in how we pull data from ensembl. PR #1671 should fix this, I think

[petrelharp]

Okay - update your github and this should work? Please let us know if there are issues with the result.

[AprilYUZhang]

Thank you! It works now.