Fusion Report fails to download references

[SPPearce]

Description of the bug

When I try and build the references, the FUSION_REPORT_DOWNLOAD module fails with a python error.

Command used and terminal output

nextflow run nf-core/rnafusion -profile crukmi --build_references --all --cosmic_username <USERNAME> --cosmic_passwd "<PASSWORD>" --genomes_base references --outdir rnafusion_references/v2.3.4

ERROR ~ Error executing process > 'NFCORE_RNAFUSION:BUILD_REFERENCES:FUSIONREPORT_DOWNLOAD (fusionreport)'

Caused by:
  Process `NFCORE_RNAFUSION:BUILD_REFERENCES:FUSIONREPORT_DOWNLOAD (fusionreport)` terminated with an error exit status (1)

Command executed:

  fusion_report download --cosmic_usr <USERNAME> --cosmic_passwd <PASSWORD>  ./
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAFUSION:BUILD_REFERENCES:FUSIONREPORT_DOWNLOAD":
      fusion_report: $(fusion_report --version | sed 's/fusion-report //')
  END_VERSIONS

Command exit status:
  1

Command output:
  Downloading resources...
  Downloading mitelman_db.zip
  near "VALUES": syntax error
  Traceback (most recent call last):
    File "/usr/local/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/common/db.py", line 71, in setup
      self.connection.executemany(
  sqlite3.OperationalError: near "VALUES": syntax error
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/usr/local/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/app.py", line 71, in run
      Download(params)
    File "/usr/local/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/download.py", line 22, in __init__
      self.download_all(params)
    File "/usr/local/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/download.py", line 41, in download_all
      Net.get_mitelman(self, return_err)
    File "/usr/local/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/common/net.py", line 211, in get_mitelman
      db.setup(files, delimiter='\t', skip_header=False, encoding='ISO-8859-1')
    File "/usr/local/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/common/db.py", line 78, in setup
      raise DbException(ex)
  fusion_report.common.exceptions.db.DbException: near "VALUES": syntax error
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/usr/local/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/EGG-INFO/scripts/fusion_report", line 13, in <module>
      app.run()
    File "/usr/local/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/app.py", line 78, in run
      raise AppException(ex)
  fusion_report.common.exceptions.app.AppException: near "VALUES": syntax error

Command error:
  near "VALUES": syntax error

Relevant files

The work directory when it fails has the following oddly named contents:

__MACOSX   
fusion_report.log   
mitelman.db  
'mitelman_db (1) 2'   
mitelman_db.zip

the 'mitelman_db (1) 2' folder contains 38 files, all *.DATA or *.SCHEMA. The __MACOSX folder contains another 'mitelman_db (1) 2' which contains hidden files e.g. ._AUTHREF.JSON.SCHEMA

System information

rnafusion v2.3.4
Nextflow v23.04.2
Apptainer v1.2.0
Slurm executor on a local HPC, using a custom config (crukmi)