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[23.0] Fix History contents genome_build filter postgresql bug #17384

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merged 3 commits into from
Feb 8, 2024
Merged

[23.0] Fix History contents genome_build filter postgresql bug #17384

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38b1107
[23.0] Fix History contents `genome_build` filter postgresql bug
ahmedhamidawan Jan 29, 2024
3e94c4d
check dbkey: [".."] as well, fix mypy errors
ahmedhamidawan Jan 30, 2024
5ffa9e1
move database_connection assignment after super()...
ahmedhamidawan Jan 30, 2024
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18 changes: 14 additions & 4 deletions lib/galaxy/managers/genomes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,10 @@
TYPE_CHECKING,
)

from sqlalchemy import func
from sqlalchemy import (
func,
text,
)

from galaxy import model as m
from galaxy.exceptions import (
Expand Down Expand Up @@ -75,6 +78,7 @@ def _get_index_filename(self, id, tbl_entries, ext, index_type):

class GenomeFilterMixin:
orm_filter_parsers: "OrmFilterParsersType"
database_connection: str
valid_ops = ("eq", "contains", "has")

def create_genome_filter(self, attr, op, val):
Expand All @@ -86,15 +90,21 @@ def _create_genome_filter(model_class=None):
# Doesn't filter genome_build for collections
if model_class.__name__ == "HistoryDatasetCollectionAssociation":
return False
column = func.json_extract(model_class.table.c._metadata, "$.dbkey")
# TODO: should use is_postgres(self.database_connection) in 23.2
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if self.database_connection.startswith("postgres"):
column = text("convert_from(metadata, 'UTF8')::json ->> 'dbkey'")
else:
column = func.json_extract(model_class.table.c._metadata, "$.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})
3 changes: 2 additions & 1 deletion lib/galaxy/managers/history_contents.py
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Expand Up @@ -632,8 +632,9 @@ def parse_type_id_list(self, type_id_list_string, sep=","):

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)
Expand Down
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