fusor test failures

fusor_test_failures.txt

[ issue-132-tests ⚙ venv] ~/code/fusor % ipython
Python 3.11.0 (main, Sep  6 2023, 12:48:52) [Clang 14.0.3 (clang-1403.0.22.14.1)]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.16.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from gene.database import create_db

In [2]: db = create_db()

In [3]: db.get_source_metadata("NCBI")
Out[3]:
{'data_license': 'custom',
 'data_license_url': 'https://www.ncbi.nlm.nih.gov/home/about/policies/',
 'version': '20231031',
 'data_url': {'info_file': 'ftp.ncbi.nlm.nih.govgene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz',
  'history_file': 'ftp.ncbi.nlm.nih.govgene/DATA/gene_history.gz',
  'assembly_file': 'ftp.ncbi.nlm.nih.govgenomes/refseq/vertebrate_mammalian/Homo_sapiens/latest_assembly_versions/'},
 'rdp_url': 'https://reusabledata.org/ncbi-gene.html',
 'data_license_attributes': {'non_commercial': False,
  'attribution': False,
  'share_alike': False},
 'genome_assemblies': ['GRCh38.p14']}

In [4]: db.get_source_metadata("HGNC")
Out[4]:
{'data_license': 'CC0',
 'data_license_url': 'https://www.genenames.org/about/license/',
 'version': '20231031',
 'data_url': {'complete_set_archive': 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json'},
 'rdp_url': None,
 'data_license_attributes': {'non_commercial': False,
  'attribution': False,
  'share_alike': False},
 'genome_assemblies': []}

In [5]: db.get_source_metadata("Ensembl")
Out[5]:
{'data_license': 'custom',
 'data_license_url': 'https://useast.ensembl.org/info/about/legal/disclaimer.html',
 'version': '110',
 'data_url': {'genome_annotations': 'ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/Homo_sapiens.GRCh38.110.gff3.gz'},
 'rdp_url': None,
 'data_license_attributes': {'non_commercial': False,
  'attribution': False,
  'share_alike': False},
 'genome_assemblies': ['GRCh38']}

In [6]: !pip show gene-normalizer
/Users/jss009/code/fusor/venv/lib/python3.11/site-packages/IPython/core/interactiveshell.py:2622: UserWarning: You executed the system command !pip which may not work as expected. Try the IPython magic %pip instead.
  warnings.warn(
Name: gene-normalizer
Version: 0.1.40.dev1
Summary: VICC normalization routines for genes
Home-page:
Author: Alex Wagner, Kori Kuzma, James Stevenson
Author-email:
License: MIT License