datanator_rest_api.routes package

Submodules

datanator_rest_api.routes.ftx module

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Author

Zhouyang Lian < zhouyang.lian@familian.life >

Date

2019-10-20

Copyright

2019, Karr Lab

License

MIT

Bases: object

class frontend_num_of_index[source]

Bases: object

get(indices, size, fields, from_=0)[source]
class gene_ranked_by_ko[source]

Bases: object

get(from_, size, fields=['*'])[source]
get(index, from_, size, fields, _source_includes=[])[source]
class indices_in_page[source]

Bases: object

get(iof, index, from_, size, fields)[source]
class num_of_index[source]

Bases: object

get(index, from_, size, fields, includes, excludes)[source]

datanator_rest_api.routes.kegg module

Metabolites collection controller This file defines the methods for the operations on the Metabolites collection. The root class contains the HTTP methods for the /metabolites/ path Any subpaths are contained in an internal class

Author

Zhouyang Lian < zhouyang.lian@familian.life >

Date

2020-02-06

Copyright

2019, Karr Lab

License

MIT

class datanator_rest_api.routes.kegg.get_meta[source]

Bases: object

get(_from=0, size=10)[source]

datanator_rest_api.routes.metabolites module

Metabolites collection controller This file defines the methods for the operations on the Metabolites collection. The root class contains the HTTP methods for the /metabolites/ path Any subpaths are contained in an internal class

Author

Bilal Shaikh < bilalshaikh42@gmail.com >

Author

Zhouyang Lian < zhouyang.lian@familian.life >

Date

2019-08-20

Copyright

2019, Karr Lab

License

MIT

class datanator_rest_api.routes.metabolites.concentration_only[source]

Bases: object

get()[source]
class datanator_rest_api.routes.metabolites.concentrations[source]

Bases: object

get(species='Escherichia coli', taxon_distance=False)[source]
class similar_compounds[source]

Bases: object

get(threshold=0.6, target_species='homo sapiens', taxon_distance=False)[source]
datanator_rest_api.routes.metabolites.get(inchi, species, last_id='000000000000000000000000', page_size=20)[source]
class datanator_rest_api.routes.metabolites.meta[source]

Bases: object

get(projection="{'_id': 0, 'kegg_meta.gene_ortholog': 0}")[source]
datanator_rest_api.routes.metabolites.post()[source]
datanator_rest_api.routes.metabolites.put(body)[source]
class datanator_rest_api.routes.metabolites.summary[source]

Bases: object

class concentration_count[source]

Bases: object

get()[source]
class curated_ref_count[source]

Bases: object

get()[source]
class ecmdb_conc_count[source]

Bases: object

get()[source]
class ecmdb_doc_count[source]

Bases: object

get()[source]
class ecmdb_ref_count[source]

Bases: object

get()[source]
class get_distinct[source]

Bases: object

get()[source]
class ymdb_conc_count[source]

Bases: object

get()[source]
class ymdb_doc_count[source]

Bases: object

get()[source]
class ymdb_ref_count[source]

Bases: object

get()[source]

datanator_rest_api.routes.proteins module

Proteins Controller

Author

Bilal Shaikh < bilalshaikh42@gmail.com > Zhouyang Lian < zhouyang.lian@familian.life >

Date

2019-08-21

Copyright

2019, Karr Lab

License

MIT

datanator_rest_api.routes.proteins.get()[source]
class datanator_rest_api.routes.proteins.meta[source]

Bases: object

class meta_combo[source]

Bases: object

get(ncbi_taxon_id=None, species_name=None, name=None)[source]
class meta_single[source]

Bases: object

get(ncbi_taxon_id=None, ko=None)[source]
datanator_rest_api.routes.proteins.post(body)[source]
class datanator_rest_api.routes.proteins.precise_abundance[source]

Bases: object

get(target_species='homo sapiens', taxon_distance=False)[source]
class datanator_rest_api.routes.proteins.proximity_abundance[source]

Bases: object

get(distance, depth)[source]
class proximity_abundance_kegg[source]

Bases: object

get(distance, anchor='homo sapiens')[source]
datanator_rest_api.routes.proteins.put(body)[source]
class datanator_rest_api.routes.proteins.related[source]

Bases: object

class related_reactions_by_kegg[source]

Bases: object

get()[source]
class related_reactions_by_uniprot[source]

Bases: object

get()[source]
class datanator_rest_api.routes.proteins.summary[source]

Bases: object

class num_abundances[source]

Bases: object

get()[source]
class num_obs_abundances[source]

Bases: object

get()[source]
class num_obs_modifications[source]

Bases: object

get()[source]
class num_organism[source]

Bases: object

get()[source]
class num_protein[source]

Bases: object

get()[source]
class num_publications[source]

Bases: object

get()[source]

datanator_rest_api.routes.reactions module

Reactions Controller

Author

Zhouyang Lian < zhouyang.lian@familian.life >

Date

2019-10-21

Copyright

2019, Karr Lab

License

MIT

datanator_rest_api.routes.reactions.get_kegg_meta(ec, projection)[source]
class datanator_rest_api.routes.reactions.kinlaw_by_name[source]

Bases: object

get(products, _from, size, bound, taxon_distance=True, species='homo sapiens', projection="{'kegg_meta.gene_ortholog': 0, 'kegg_meta._id': 0, '_id': 0}")[source]
class datanator_rest_api.routes.reactions.kinlaw_by_rxn[source]

Bases: object

get(products, _from, size, bound, dof, taxon_distance=False, species='homo sapiens', projection="{'kegg_meta.gene_ortholog': 0, 'kegg_meta._id': 0, '_id': 0}")[source]
class datanator_rest_api.routes.reactions.kinlaw_doc[source]

Bases: object

get(_from, size)[source]
class with_prm[source]

Bases: object

get(_from=0, size=10)[source]
class datanator_rest_api.routes.reactions.kinlaw_entry[source]

Bases: object

get(target_organism=None, last_id=0, size=10)[source]
class datanator_rest_api.routes.reactions.summary[source]

Bases: object

class get_brenda_obs[source]

Bases: object

get()[source]
class get_distinct[source]

Bases: object

get()[source]
class get_frequency[source]

Bases: object

get()[source]
class get_sabio_obs[source]

Bases: object

get()[source]
class num_entries[source]

Bases: object

get()[source]
class num_organism[source]

Bases: object

get()[source]
class num_parameter_kcat[source]

Bases: object

get()[source]
class num_parameter_km[source]

Bases: object

get()[source]
class num_refs[source]

Bases: object

get()[source]

datanator_rest_api.routes.rna module

RNA Controller

Author

Zhouyang Lian < zhouyang.lian@familian.life >

Date

2019-08-21

Copyright

2019, Karr Lab

License

MIT

datanator_rest_api.routes.rna.append_taxon_distance(doc, result, species)[source]
datanator_rest_api.routes.rna.get_kegg_meta(ko)[source]
class datanator_rest_api.routes.rna.halflife[source]

Bases: object

class get_info_by_ko[source]

Bases: object

get(_from=0, size=10, taxon_distance=True, species='homo sapiens')[source]
class get_info_by_name[source]

Bases: object

get(_from=0, size=10, taxon_distance=True, species='homo sapiens')[source]
class get_info_by_uniprot[source]

Bases: object

get(_from=0, size=10, taxon_distance=True, species='homo sapiens')[source]
class datanator_rest_api.routes.rna.modification[source]

Bases: object

class get_modifications_by_ko[source]

Bases: object

get(_from=0, size=10, target_organism='Escherichia coli', taxon_distance=False)[source]
class datanator_rest_api.routes.rna.summary[source]

Bases: object

class get_distinct[source]

Bases: object

get()[source]
class get_publication_num[source]

Bases: object

get()[source]
class get_total_docs[source]

Bases: object

get()[source]
class get_total_halflife_obs[source]

Bases: object

get()[source]
class get_total_modifications[source]

Bases: object

get()[source]

datanator_rest_api.routes.status module

Datanator Controller

Author

Bilal Shaikh < bilalshaikh42@gmail.com >

Date

2019-08-21

Copyright

2019, Karr Lab

License

MIT

datanator_rest_api.routes.status.get()[source]
datanator_rest_api.routes.status.post(body)[source]
datanator_rest_api.routes.status.put(body)[source]

datanator_rest_api.routes.taxon module

Reactions Controller

Author

Zhouyang Lian < zhouyang.lian@familian.life >

Date

2019-10-28

Copyright

2019, Karr Lab

License

MIT

class datanator_rest_api.routes.taxon.canon_rank_common_distance[source]

Bases: object

get(org_1)[source]
class datanator_rest_api.routes.taxon.canon_rank_distance[source]

Bases: object

get()[source]
class datanator_rest_api.routes.taxon.canon_rank_distance_by_name[source]

Bases: object

get()[source]
class datanator_rest_api.routes.taxon.is_child[source]

Bases: object

get(target_tax_id)[source]
class datanator_rest_api.routes.taxon.summary[source]

Bases: object

class taxon_distribution[source]

Bases: object

get()[source]

Module contents

__init__

Author

Bilal Shaikh < bilalshaikh42@gmail.com >

Date

2019-08-20

Copyright

2019, Karr Lab

License

MIT

datanator_rest_api.routes.get()[source]