Make search work on sqlite and postgres (615d1c79) · Commits · NDIP / Galaxy

lib/galaxy/managers/jobs.py

+23 −33

Original line number	Diff line number	Diff line
		@@ -366,6 +366,7 @@ class JobSearch:
		id_encoding_helper: IdEncodingHelper,
		):
		self.sa_session = sa_session
		self.dialect_name = sa_session.get_bind().dialect.name
		self.hda_manager = hda_manager
		self.dataset_collection_manager = dataset_collection_manager
		self.ldda_manager = ldda_manager
		@@ -747,6 +748,12 @@ class JobSearch:
		used_ids.append(labeled_col)
		return stmt

		def agg_expression(self, column):
		if self.dialect_name == "sqlite":
		return func.group_concat(column)
		else:
		return func.array_agg(column, order_by=column)

		def _build_stmt_for_hdca(
		self, stmt, data_conditions, used_ids, k, v, user_id, value_index, require_name_match=True
		):
		@@ -853,13 +860,7 @@ class JobSearch:
		# This CTE aggregates the path signature strings of the reference HDCA into a
		# canonical, sorted array. This array represents the complete "signature" of the collection.
		reference_full_signature_cte = (
		select(
		func.array_agg(
		sqlalchemy.text(
		f"{signature_elements_cte.c.path_signature_string.name} ORDER BY {signature_elements_cte.c.path_signature_string.name}"
		)
		).label("signature_array")
		)
		select(self.agg_expression(signature_elements_cte.c.path_signature_string).label("signature_array"))
		.select_from(signature_elements_cte)
		.cte(f"reference_full_signature_{k}_{value_index}")
		)
		@@ -946,11 +947,9 @@ class JobSearch:
		candidate_full_signatures_cte = (
		select(
		candidate_signature_elements_cte.c.candidate_hdca_id,
		func.array_agg(
		sqlalchemy.text(
		f"{candidate_signature_elements_cte.c.path_signature_string.name} ORDER BY {candidate_signature_elements_cte.c.path_signature_string.name}"
		)
		).label("full_signature_array"),
		self.agg_expression(candidate_signature_elements_cte.c.path_signature_string).label(
		"full_signature_array"
		),
		)
		.select_from(candidate_signature_elements_cte)
		.group_by(candidate_signature_elements_cte.c.candidate_hdca_id)
		@@ -1099,16 +1098,12 @@ class JobSearch:
		# used for direct comparison with candidate collections.
		reference_full_signature_cte = (
		select(
		func.array_agg(
		reference_dce_signature_elements_cte.c.path_signature_string,
		order_by=reference_dce_signature_elements_cte.c.path_signature_string,
		).label("signature_array"),
		func.array_agg(
		reference_dce_signature_elements_cte.c.raw_dataset_id_for_ordering.cast(
		sqlalchemy.Integer
		), # Cast to Integer here
		order_by=reference_dce_signature_elements_cte.c.path_signature_string, # Order by full path to ensure consistency
		).label("ordered_dataset_id_array"),
		self.agg_expression(reference_dce_signature_elements_cte.c.path_signature_string).label(
		"signature_array"
		),
		self.agg_expression(reference_dce_signature_elements_cte.c.raw_dataset_id_for_ordering).label(
		"ordered_dataset_id_array"
		),
		func.count(reference_dce_signature_elements_cte.c.path_signature_string).label(
		"element_count"
		), # Count elements based on path_signature_string
		@@ -1227,12 +1222,9 @@ class JobSearch:
		select(
		candidate_dce_signature_elements_cte.c.candidate_dce_id,
		# Corrected array_agg syntax: pass column directly, use order_by keyword
		func.array_agg(
		candidate_dce_signature_elements_cte.c.dataset_id_for_ordered_array.cast(
		sqlalchemy.Integer
		), # Cast explicitly
		order_by=candidate_dce_signature_elements_cte.c.path_signature_string, # Order by the full path
		).label("candidate_ordered_dataset_ids_array"),
		self.agg_expression(candidate_dce_signature_elements_cte.c.dataset_id_for_ordered_array).label(
		"candidate_ordered_dataset_ids_array"
		),
		func.count(candidate_dce_signature_elements_cte.c.candidate_dce_id).label(
		"candidate_element_count"
		),
		@@ -1269,11 +1261,9 @@ class JobSearch:
		final_candidate_signatures_cte = (
		select(
		candidate_dce_signature_elements_cte.c.candidate_dce_id,
		func.array_agg(
		sqlalchemy.text(
		f"{candidate_dce_signature_elements_cte.c.path_signature_string} ORDER BY {candidate_dce_signature_elements_cte.c.path_signature_string.name}"
		)
		).label("full_signature_array"),
		self.agg_expression(candidate_dce_signature_elements_cte.c.path_signature_string).label(
		"full_signature_array"
		),
		)
		.select_from(candidate_dce_signature_elements_cte)
		.where(

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