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ipr.main

CACHE_GENE_MINIMUM

CACHE_GENE_MINIMUM = 5000

clean_unsupported_content()

Remove unsupported content. This content is either added to facilitate creation or to support upcoming and soon to be supported content that we would like to implement but is not yet supported by the upload

def clean_unsupported_content(upload_content: Dict) -> Dict:

Args

  • upload_content (Dict)

Returns

  • Dict

create_report()

Run the matching and create the report JSON for upload to IPR

def create_report(
    username: str,
    password: str,
    content: Dict,
    ipr_url: str = DEFAULT_URL,
    log_level: str = 'info',
    output_json_path: str = None,
    always_write_output_json: bool = False,
    ipr_upload: bool = True,
    interactive: bool = False,
    graphkb_url: str = '',
    generate_therapeutics: bool = False,
    generate_comments: bool = True,
) -> Dict:

Args

  • username (str): the username for connecting to GraphKB and IPR
  • password (str): the password for connecting to GraphKB and IPR
  • content (Dict): report content
  • ipr_url (str): base URL to use in connecting to IPR
  • log_level (str): the logging level
  • output_json_path (str): path to a JSON file to output the report upload body.
  • always_write_output_json (bool): with successful IPR upload
  • ipr_upload (bool): upload report to ipr
  • interactive (bool): progressbars for interactive users
  • graphkb_url (str)
  • generate_therapeutics (bool): create therapeutic options for upload with the report
  • generate_comments (bool): create the analyst comments section for upload with the report

Returns

  • Dict: ipr_conn.upload_report return dictionary
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