3.1. datanator_query_python package

3.1.1. Subpackages

• 3.1.1.1. datanator_query_python.aggregate package
  • 3.1.1.1.1. Submodules
  • 3.1.1.1.2. datanator_query_python.aggregate.lookups module
  • 3.1.1.1.3. datanator_query_python.aggregate.pipelines module
  • 3.1.1.1.4. datanator_query_python.aggregate.tabu module
  • 3.1.1.1.5. Module contents
• 3.1.1.2. datanator_query_python.config package
  • 3.1.1.2.1. Submodules
  • 3.1.1.2.2. datanator_query_python.config.config module
  • 3.1.1.2.3. datanator_query_python.config.motor_client_manager module
  • 3.1.1.2.4. datanator_query_python.config.query_manager module
  • 3.1.1.2.5. datanator_query_python.config.query_schema_2_manager module
  • 3.1.1.2.6. Module contents
• 3.1.1.3. datanator_query_python.query package
  • 3.1.1.3.1. Submodules
  • 3.1.1.3.2. datanator_query_python.query.full_text_search module
  • 3.1.1.3.3. datanator_query_python.query.query_corum module
  • 3.1.1.3.4. datanator_query_python.query.query_intact_complex module
  • 3.1.1.3.5. datanator_query_python.query.query_kegg_organism_code module
  • 3.1.1.3.6. datanator_query_python.query.query_kegg_orthology module
  • 3.1.1.3.7. datanator_query_python.query.query_metabolite_concentrations module
  • 3.1.1.3.8. datanator_query_python.query.query_metabolites module
  • 3.1.1.3.9. datanator_query_python.query.query_metabolites_meta module
  • 3.1.1.3.10. datanator_query_python.query.query_pax module
  • 3.1.1.3.11. datanator_query_python.query.query_protein module
  • 3.1.1.3.12. datanator_query_python.query.query_rna_halflife module
  • 3.1.1.3.13. datanator_query_python.query.query_sabio_compound module
  • 3.1.1.3.14. datanator_query_python.query.query_sabio_reaction_entries module
  • 3.1.1.3.15. datanator_query_python.query.query_sabiork module
  • 3.1.1.3.16. datanator_query_python.query.query_sabiork_old module
  • 3.1.1.3.17. datanator_query_python.query.query_taxon_tree module
  • 3.1.1.3.18. datanator_query_python.query.query_uniprot module
  • 3.1.1.3.19. datanator_query_python.query.query_uniprot_org module
  • 3.1.1.3.20. datanator_query_python.query.query_xmdb module
  • 3.1.1.3.21. Module contents
• 3.1.1.4. datanator_query_python.query_schema_2 package
  • 3.1.1.4.1. Submodules
  • 3.1.1.4.2. datanator_query_python.query_schema_2.ftx_search module
  • 3.1.1.4.3. datanator_query_python.query_schema_2.query_entity module
  • 3.1.1.4.4. datanator_query_python.query_schema_2.query_observation module
  • 3.1.1.4.5. datanator_query_python.query_schema_2.query_taxon_tree_v2 module
  • 3.1.1.4.6. datanator_query_python.query_schema_2.query_uniprot_v2 module
  • 3.1.1.4.7. Module contents
• 3.1.1.5. datanator_query_python.util package
  • 3.1.1.5.1. Submodules
  • 3.1.1.5.2. datanator_query_python.util.base26 module
  • 3.1.1.5.3. datanator_query_python.util.chem_util module
  • 3.1.1.5.4. datanator_query_python.util.file_util module
  • 3.1.1.5.5. datanator_query_python.util.mapper_reducer module
  • 3.1.1.5.6. datanator_query_python.util.mongo_util module
  • 3.1.1.5.7. datanator_query_python.util.motor_util module
  • 3.1.1.5.8. datanator_query_python.util.parse_heroku_logs module
  • 3.1.1.5.9. Module contents

3.1.2. Submodules

3.1.3. datanator_query_python.__main__ module

datanator_query_python command line interface

Author

Name <email>

Date

2019-8-26

Copyright

2019, Karr Lab

License

MIT

class datanator_query_python.__main__.App(label=None, **kw)

Bases: cement.core.foundation.App

Command line application

class Meta

Bases: object

base_controller = 'base'

handlers = [<class 'datanator_query_python.__main__.BaseController'>, <class 'datanator_query_python.__main__.DefineSchema'>]

label = 'datanator_query_python'

class datanator_query_python.__main__.BaseController(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

Base controller for command line application

class Meta

Bases: object

arguments = [(['-v', '--version'], {'action': 'version', 'version': '0.7.0'})]

description = 'datanator_query_python'

label = 'base'

class datanator_query_python.__main__.DefineSchema(*args, **kw)

Bases: cement.ext.ext_argparse.ArgparseController

Karrlab elasticsearch delete index.

class Meta

Bases: object

arguments = [(['db'], {'type': <class 'str'>, 'help': 'Name of the database in which the collection resides.'}), (['collection'], {'type': <class 'str'>, 'help': 'Name of the collection to be defined.'}), (['jsonschema'], {'type': <class 'str'>, 'help': 'Location of jsonschema'}), (['--config_name', '-cn'], {'type': <class 'str'>, 'default': 'TestConfig', 'help': 'Config class to be used.'})]

description = 'Define jsonschema of a collection'

label = 'mongo-def-schema'

stacked_on = 'base'

stacked_type = 'nested'

datanator_query_python.__main__.main()

3.1.4. datanator_query_python._version module

3.1.5. Module contents