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

Form aggregate lookup objects

class datanator_query_python.aggregate.lookups.Lookups

Bases: object

complex_lookup(_from, let, pipeline, _as)

Complex lookup object (lookups with let).

Parameters

• _from (str) – collection to join.

• let (Obj) – specifies variables to use in pipeline stages.

• pipeline (list of Obj) – specifies the pipeline to run on the joined collection.

• _as (str) – output array field.

simple_lookup(_from, local_field, foreign_field, _as)

Simple look up operation (without let or pipeline).

Parameters

• _from (str) – collection to join.

• local_field (str) – field from input documents.

• foreign_field (str) – field from the documents of the “_from” collection.

• _as (str) – output array field.

Returns

(Obj)

3.1.1.1.3. datanator_query_python.aggregate.pipelines module

Various aggregation pipelines

class datanator_query_python.aggregate.pipelines.Pipeline

Bases: object

aggregate_all_occurences(field, match=None, project_post={'count': 1}, group=None, unwind=None)

Aggregate all occurences of values in field.

Parameters

• field (str) – Name of the field.

• match (Obj) – Filtering of unnecessary data.

• project (Obj) – remove fields before matching.

• group (Obj) – additional group parameters.

• unwind (Obj) – Unwind operation if field of interest is in subdocuments.

Returns

(list)

aggregate_common_canon_ancestors(anchor, target, org_format='tax_id', intersect_name='anc_match')

Get common canonical ancestors between two organisms.

Parameters

• anchor (Obj) – document of anchor organism.

• target (str or int) – target organism.

• org_format (str, optional) – field used to identify organism (tax_id or tax_name).

• intersect_name (str) – name for intersection array.

Returns

(list)

aggregate_field_count(field, projection={'parameter': 1}, match={'parameter.observed_name': 'Ki'}, unwind=None, group={'$group': {'count': {'$sum': 1}}})

Aggregate number of occurences of a value in field.

Parameters

• field (str) – field of interest.

• projection (Obj) – Projection (prune unnecessary data in document).

• match (Obj) – Further filtering of data that meet certain conditions.

Returns

(list)

aggregate_kegg_orthology(expr, projection={'_id': 0, 'gene_ortholog': 0})

Aggregate kegg orthology information

Parameters

• expr (Obj) – match expression.

• projection (Obj, optional) – projection in pipeline.

Returns

(list)

aggregate_taxon_distance(match, local_field, _as, anchor, target, org_format='tax_id', intersect_name='anc_match')

Aggrate canonical taxon distance information for frontend (avoiding iteration)

Parameters

• match (Obj) – match object in pipeline.

• local_field (str) – field from input documents.

• _as (str) – output array.

• anchor (Obj) – document of anchor organism.

• target (str or int) – target organism.

• org_format (str, optional) – field used to identify organism (tax_id or tax_name).

• intersect_name (str) – name for intersection array.

Returns

(list)

aggregate_total_array_length(field)

Aggregate the total length of an array field in collection. e.g. [{“field”: [0, 1]}, {“field”: [2]}]

Parameters

field (str) – Name of the field.

Returns

(list)

3.1.1.1.4. datanator_query_python.aggregate.tabu module

Tabulate taxonomic distribution of all observations across relevant collections. https://github.com/KarrLab/datanator_rest_api/issues/97

class datanator_query_python.aggregate.tabu.Tabu(MongoDB=None, db=None, username=None, password=None, authSource=None, readPreference=None, max_entries=inf, verbose=True)

Bases: datanator_query_python.util.mongo_util.MongoUtil

taxon_dist(collection, field, match=None, unwind=None)

Generalized version of uniprot_taxon_dist.

Parameters

• collection (str) – name of collection.

• field (str) – Field upon which aggregation will be done.

• match (Obj) – Filtering of unnecessary data.

• unwind (Obj) – Unwind operation if field of interest is in subdocuments.

Returns

(CommandCursor)

uniprot_taxon_dist()

Tabulate uniprot collections taxonomic distribution.

Returns

(CommandCursor)

datanator_query_python.aggregate.tabu.main()

3.1.1.1.5. Module contents