From ed72a2bf0cd0c9863444f5b96de9302c7bd4a590 Mon Sep 17 00:00:00 2001 From: Alexander Berger Date: Fri, 10 May 2024 13:07:41 -0400 Subject: [PATCH] Adding the ontology term filter to genesets --- poetry.lock | 21 ++++++++++++++++----- pyproject.toml | 4 ++-- src/geneweaver/api/controller/genesets.py | 2 ++ src/geneweaver/api/services/geneset.py | 5 +++++ 4 files changed, 25 insertions(+), 7 deletions(-) diff --git a/poetry.lock b/poetry.lock index 094ed37..65d039a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "anyio" @@ -514,13 +514,13 @@ requests = ">=2.31.0,<3.0.0" [[package]] name = "geneweaver-db" -version = "0.3.4" +version = "0.4.0a1" description = "Database Interaction Services for GeneWeaver" optional = false python-versions = "<4.0,>=3.9" files = [ - {file = "geneweaver_db-0.3.4-py3-none-any.whl", hash = "sha256:af53696ec40e7761e52127adf9b04a68503b38a9d1101d2815e4476b62b458b3"}, - {file = "geneweaver_db-0.3.4.tar.gz", hash = "sha256:a268b406a714604f3404e06215bfc5d98fd3e9ba0f05a0dbf2bdaeeb5e4a20bd"}, + {file = "geneweaver_db-0.4.0a1-py3-none-any.whl", hash = "sha256:220587d957d744fd4278d13d63b993d8f03375f2b8fc193df79258206305fa87"}, + {file = "geneweaver_db-0.4.0a1.tar.gz", hash = "sha256:679da8cdcfdf686045857293d901c35d441d70ef8d3f4c9bc7bd7c7e6989fda0"}, ] [package.dependencies] @@ -1432,6 +1432,7 @@ files = [ {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = 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"geneweaver-api" -version = "0.5.0a1" +version = "0.6.0a0" description = "The Geneweaver API" authors = [ "Alexander Berger ", @@ -20,7 +20,7 @@ python = "^3.9" geneweaver-core = "^0.9.1" fastapi = {extras = ["all"], version = "^0.99.1"} uvicorn = {extras = ["standard"], version = "^0.24.0"} -geneweaver-db = "^0.3.4" +geneweaver-db = "0.4.0a1" psycopg-pool = "^3.1.7" requests = "^2.31.0" python-jose = {extras = ["cryptography"], version = "^3.3.0"} diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py index 5cd04c2..faed7f2 100644 --- a/src/geneweaver/api/controller/genesets.py +++ b/src/geneweaver/api/controller/genesets.py @@ -63,6 +63,7 @@ def get_visible_genesets( ), ] = None, gene_id_type: Optional[GeneIdentifier] = None, + ontology_term: Optional[str] = None, search_text: Annotated[ Optional[str], Query(description=api_message.SEARCH_TEXT) ] = None, @@ -102,6 +103,7 @@ def get_visible_genesets( gene_id_type=gene_id_type, search_text=search_text, with_publication_info=with_publication_info, + ontology_term=ontology_term, only_my_genesets=only_my_genesets, limit=limit, offset=offset, diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py index ba4ccf1..7d75849 100644 --- a/src/geneweaver/api/services/geneset.py +++ b/src/geneweaver/api/services/geneset.py @@ -27,6 +27,7 @@ def get_visible_genesets( pubmed_id: Optional[int] = None, gene_id_type: Optional[GeneIdentifier] = None, search_text: Optional[str] = None, + ontology_term: Optional[str] = None, limit: Optional[int] = None, offset: Optional[int] = None, with_publication_info: bool = True, @@ -34,7 +35,9 @@ def get_visible_genesets( """Get genesets from the database. :param cursor: A database cursor. + :param user: The user requesting the genesets. :param gs_id: Show only results with this geneset ID. + :param only_my_genesets: Show only results owned by the user. :param curation_tier: Show only results of this curation tier. :param species: Show only results associated with this species. :param name: Show only results with this name. @@ -44,6 +47,7 @@ def get_visible_genesets( :param gene_id_type: Show only results with this gene ID type. :param search_text: Return genesets that match this search text (using PostgreSQL full-text search). + :param ontology_term: Show only results associated with this ontology term. :param limit: Limit the number of results. :param offset: Offset the results. :param with_publication_info: Include publication info in the return. @@ -70,6 +74,7 @@ def get_visible_genesets( gene_id_type=gene_id_type, search_text=search_text, with_publication_info=with_publication_info, + ontology_term=ontology_term, limit=limit, offset=offset, )