Database Manager
PathMe-Viewer database manager.
This module contains the PathMe database manager.
-
class
pathme_viewer.manager.Manager(engine, session)[source]
Database manager.
Init PathMe manager.
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create_all(check_first=True)[source]
Create tables for PathMe.
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drop_all(check_first=True)[source]
Drop all tables for PathMe.
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count_pathways()[source]
Count the pathways in the database.
- Return type
int
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count_pathways_by_resource()[source]
Count the pathways in the database grouping by resource.
- Return type
int
-
get_all_pathways()[source]
Get all pathways in the database.
- Return type
list[Pathway]
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get_all_pathway_graphs()[source]
Get all pathway graphs.
- Return type
list[pybel.BELGraph]
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get_pathway_by_id(pathway_id, resource_name)[source]
Get pathway by canonical identifier.
- Parameters
-
- Return type
Optional[Pathway]
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get_pathway_by_name(pathway_name, resource_name)[source]
Get pathway by name.
- Parameters
-
- Return type
Optional[Pathway]
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get_pathways_from_resource(resource_name)[source]
Get pathways from a given database.
- Parameters
resource_name (str) – name of the database
- Return type
Optional[list[Pathway]]
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create_pathway(pathway_dict)[source]
Create pathway.
- Parameters
pathway_dict (dict) – pathway identifier
- Return type
Pathway
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delete_pathway(pathway_id, resource_name)[source]
Delete a pathway.
- Parameters
-
- Return type
bool
-
delete_all_pathways()[source]
Delete all the pathways.
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delete_pathways_from_resource(resource_name)[source]
Delete pathways from a given database.
- Parameters
resource_name (str) – name of the database
- Return type
bool
-
get_or_create_pathway(pathway_dict)[source]
Get or create pathway.
- Parameters
pathway_dict (dict) – pathway info
- Return type
Pathway
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query_pathway_by_name(query, limit=None)[source]
Return all pathways having the query in their names.
- Parameters
-
- Return type
list[Pathway]
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query_pathway_by_name_and_resource(query, resource_name, limit=None)[source]
Return all pathways having the query in their names.
- Parameters
query (str) – query string
resource_name (str) – database name
limit (Optional[int]) – limit result query
- Return type
list[Pathway]