API Reference

• Graph Database Connector (graphdb_connector)
  • connector.py
  • query_utils.py
• Graph Database Builder (graphdb_builder)
  • Ontology Databases
    • Ontologies Parsers
      • efoParser.py
      • icdParser.py
      • oboParser.py
      • reflectParser.py
      • snomedParser.py
    • ontologies_controller.py
  • Biomedical Databases
    • Biomedical Databases Parsers
      • cancerGenomeInterpreterParser.py
      • corumParser.py
      • disgenetParser.py
      • drugBankParser.py
      • drugGeneInteractionDBParser.py
      • exposomeParser.py
      • foodbParser.py
      • goaParser.py
      • gwasCatalogParser.py
      • hgncParser.py
      • hmdbParser.py
      • hpaParser.py
      • intactParser.py
      • jensenlabParser.py
      • mutationDsParser.py
      • oncokbParser.py
      • pathwayCommonsParser.py
      • pfamParser.py
      • pspParser.py
      • reactomeParser.py
      • refseqParser.py
      • siderParser.py
      • signorParser.py
      • smpdbParser.py
      • stringParser.py
      • textminingParser.py
      • uniprotParser.py
    • databases_controller.py
  • Experimental Data
    • Experimental Data Parsers
      • clinicalParser.py
      • proteomicsParser.py
      • wesParser.py
    • experiments_controller.py
  • User Creation
    • users_controller.py
  • CKG Builder
    • create_user.py
    • importer.py
    • loader.py
    • builder.py
  • builder_utils.py
  • mapping.py
• Report Manager (report_manager)
  • Apps
    • basicApp.py
    • dataUploadApp.py
    • dataUpload.py
    • homepageApp.py
    • homepageStats.py
    • importsApp.py
    • imports.py
    • initialApp.py
    • loginApp.py
    • projectApp.py
    • projectCreationApp.py
    • projectCreation.py
  • app.py
  • dataset.py
  • index.py
  • knowledge.py
  • project.py
  • report.py
  • user.py
  • utils.py
  • worker.py
• Analytics Core (analytics_core)
  • Analytics
    • analytics.py
    • wgcnaAnalysis.py
    • kaplan_meierAnalysis.py
  • Viz
    • viz.py
    • wgcnaFigures.py
    • Dendrogram.py
    • color_list.py
  • R_wrapper.py
  • analytics_factory.py
  • utils.py
• Notebooks - development
  • vis.py

ckg_utils.py

read_ckg_config(key=None)

save_dict_to_yaml(data, yaml_file)

read_yaml(yaml_file)

get_queries(queries_file)

get_configuration(configuration_file)

get_configuration_variable(configuration_file, variable)

setup_logging(path='log.config', key=None)

Setup logging configuration

listDirectoryFiles(directory)

listDirectoryFolders(directory)

checkDirectory(directory)

is_jsonable(x)

convert_dash_to_json(dash_object)

class NumpyEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Bases: json.encoder.JSONEncoder

default(obj)

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)

class DictDFEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Bases: json.encoder.JSONEncoder

default(obj)

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)