Unverified Commit 4c1c8e22 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #17384 from ahmedhamidawan/fix_genome_build_filter_postgres 

[23.0] Fix History contents `genome_build` filter postgresql bug
parents c654c886 5ffa9e15

lib/galaxy/managers/genomes.py

+14 −4
Original line number Diff line number Diff line
@@ -4,7 +4,10 @@ from typing import ( 
    TYPE_CHECKING,

)



from sqlalchemy import func

from sqlalchemy import (

    func,

    text,

)



from galaxy import model as m

from galaxy.exceptions import (
@@ -75,6 +78,7 @@ class GenomesManager: 


class GenomeFilterMixin:

    orm_filter_parsers: "OrmFilterParsersType"

    database_connection: str

    valid_ops = ("eq", "contains", "has")



    def create_genome_filter(self, attr, op, val):
@@ -86,15 +90,21 @@ class GenomeFilterMixin: 
            # Doesn't filter genome_build for collections

            if model_class.__name__ == "HistoryDatasetCollectionAssociation":

                return False

            # TODO: should use is_postgres(self.database_connection) in 23.2

            if self.database_connection.startswith("postgres"):

                column = text("convert_from(metadata, 'UTF8')::json ->> 'dbkey'")

            else:

                column = func.json_extract(model_class.table.c._metadata, "$.dbkey")

            lower_val = val.lower()  # Ignore case

            # dbkey can either be "hg38" or '["hg38"]', so we need to check both

            if op == "eq":

                cond = func.lower(column) == lower_val

                cond = func.lower(column) == lower_val or func.lower(column) == f'["{lower_val}"]'

            else:

                cond = func.lower(column).contains(lower_val, autoescape=True)

            return cond



        return _create_genome_filter



    def _add_parsers(self):

    def _add_parsers(self, database_connection: str):

        self.database_connection = database_connection

        self.orm_filter_parsers.update({"genome_build": self.create_genome_filter})

lib/galaxy/managers/history_contents.py

+2 −1
Original line number Diff line number Diff line
@@ -632,8 +632,9 @@ class HistoryContentsFilters( 


    def _add_parsers(self):

        super()._add_parsers()

        database_connection: str = self.app.config.database_connection

        annotatable.AnnotatableFilterMixin._add_parsers(self)

        genomes.GenomeFilterMixin._add_parsers(self)

        genomes.GenomeFilterMixin._add_parsers(self, database_connection)

        deletable.PurgableFiltersMixin._add_parsers(self)

        taggable.TaggableFilterMixin._add_parsers(self)

        tools.ToolFilterMixin._add_parsers(self)