datanator_rest_api.routes package¶

Submodules¶

datanator_rest_api.routes.ftx module¶

Full text search perform full text search

Author: Zhouyang Lian < zhouyang.lian@familian.life >
Date: 2019-10-20
Copyright: 2019, Karr Lab
License: MIT

class datanator_rest_api.routes.ftx.text_search[source]¶

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]¶