diff --git a/big_scape/cli/cli_common_options.py b/big_scape/cli/cli_common_options.py
index 0969b1cf..cf556b5c 100644
--- a/big_scape/cli/cli_common_options.py
+++ b/big_scape/cli/cli_common_options.py
@@ -273,21 +273,6 @@ def common_cluster_query(fn):
"based on the generic 'mix' weights."
),
),
- click.option(
- "--legacy_classify",
- is_flag=True,
- help=(
- "Does not use antiSMASH BGC classes to run analyses on "
- "class-based bins, instead it uses BiG-SCAPE v1 predefined groups: "
- "PKS1, PKSOther, NRPS, NRPS-PKS-hybrid, RiPP, Saccharide, Terpene, Others. "
- "Will also use BiG-SCAPE v1 legacy_weights for distance calculations. "
- "This feature is available for backwards compatibility with "
- "antiSMASH versions up to v7. For higher antiSMASH versions, use "
- "at your own risk, as BGC classes may have changed. All antiSMASH "
- "classes that this legacy mode does not recognize will be grouped in "
- "'others'."
- ),
- ),
click.option(
"--alignment_mode",
type=click.Choice(["global", "glocal", "local", "auto"]),
@@ -339,7 +324,7 @@ def common_cluster_query(fn):
"-db",
"--db_path",
type=click.Path(path_type=Path, dir_okay=False),
- help="Path to sqlite db output file. (default: output_dir/data_sqlite.db).",
+ help="Path to sqlite db output file. (default: output_dir/output_dir.db).",
),
# TODO: implement cand_cluster here and LCS-ext
click.option(
diff --git a/big_scape/cli/cli_validations.py b/big_scape/cli/cli_validations.py
index 1a4f0d92..796ce8bc 100644
--- a/big_scape/cli/cli_validations.py
+++ b/big_scape/cli/cli_validations.py
@@ -112,7 +112,7 @@ def validate_output_paths(ctx) -> None:
timestamp = time.strftime("%Y-%m-%d_%H-%M-%S", time.localtime())
if "db_path" in ctx.obj and ctx.obj["db_path"] is None:
- db_path = ctx.obj["output_dir"] / Path("data_sqlite.db")
+ db_path = ctx.obj["output_dir"] / Path(f"{ctx.obj['output_dir'].name}.db")
ctx.obj["db_path"] = db_path
if "log_path" in ctx.obj and ctx.obj["log_path"] is None:
diff --git a/big_scape/cli/cluster_cli.py b/big_scape/cli/cluster_cli.py
index 373f4bbc..16b497a9 100644
--- a/big_scape/cli/cluster_cli.py
+++ b/big_scape/cli/cluster_cli.py
@@ -35,6 +35,21 @@
)
# binning parameters
@click.option("--no_mix", is_flag=True, help=("Don't run the all-vs-all analysis."))
+@click.option(
+ "--legacy_classify",
+ is_flag=True,
+ help=(
+ "Does not use antiSMASH BGC classes to run analyses on "
+ "class-based bins, instead it uses BiG-SCAPE v1 predefined groups: "
+ "PKS1, PKSOther, NRPS, NRPS-PKS-hybrid, RiPP, Saccharide, Terpene, Others. "
+ "Will also use BiG-SCAPE v1 legacy_weights for distance calculations. "
+ "This feature is available for backwards compatibility with "
+ "antiSMASH versions up to v7. For higher antiSMASH versions, use "
+ "at your own risk, as BGC classes may have changed. All antiSMASH "
+ "classes that this legacy mode does not recognize will be grouped in "
+ "'others'."
+ ),
+)
# networking parameters
@click.option(
"--include_singletons",
diff --git a/big_scape/cli/query_cli.py b/big_scape/cli/query_cli.py
index 71fa20d6..011d9901 100644
--- a/big_scape/cli/query_cli.py
+++ b/big_scape/cli/query_cli.py
@@ -49,14 +49,13 @@
),
)
@click.option(
- "--skip_propagation",
+ "--propagate",
is_flag=True,
help=(
- "Only generate edges between the query and reference BGCs. If not set, "
- "BiG-SCAPE will also propagate edge generation to reference BGCs. "
- "Warning: if the database already contains all edges, this will not work, "
- "and the output will still showcase all edges between nodes "
- "in the query connected component."
+ "By default, BiG-SCAPE will only generate edges between the query and reference"
+ " BGCs. With the propagate flag, BiG-SCAPE will go through multiple cycles of "
+ "edge generation until no new reference BGCs are connected to the query "
+ "connected component."
),
)
@click.pass_context
@@ -74,6 +73,7 @@ def query(ctx, *args, **kwarg):
ctx.obj.update(ctx.params)
ctx.obj["no_mix"] = None
ctx.obj["hybrids_off"] = False
+ ctx.obj["legacy_classify"] = False
ctx.obj["mode"] = "Query"
# workflow validations
diff --git a/big_scape/comparison/binning.py b/big_scape/comparison/binning.py
index 404b2ebc..b6bde73a 100644
--- a/big_scape/comparison/binning.py
+++ b/big_scape/comparison/binning.py
@@ -133,7 +133,7 @@ def num_pairs(self) -> int:
# find a collection of gbks with more than one subrecord
member_table = (
select(func.count(record_table.c.gbk_id).label("rec_count"))
- .where(record_table.c.record_type == self.record_type.value)
+ .where(record_table.c.id.in_(self.record_ids))
.group_by(record_table.c.gbk_id)
.having(func.count() > 1)
.subquery()
@@ -406,8 +406,9 @@ def __init__(
label: str,
edge_param_id: int,
weights: str,
+ record_type: Optional[RECORD_TYPE],
):
- super().__init__(label, edge_param_id, weights)
+ super().__init__(label, edge_param_id, weights, record_type)
self.reference_records: set[BGCRecord] = set()
self.done_records: set[BGCRecord] = set()
self.working_query_records: set[BGCRecord] = set()
@@ -426,6 +427,9 @@ def generate_pairs(
if record_a == record_b:
continue
+ if record_a.parent_gbk == record_b.parent_gbk:
+ continue
+
if legacy_sorting:
sorted_a, sorted_b = sorted((record_a, record_b), key=sort_name_key)
if sorted_a._db_id is None or sorted_b._db_id is None:
@@ -455,6 +459,48 @@ def num_pairs(self) -> int:
num_pairs = num_query_records * num_ref_records
+ # delete pairs originating from the same parent gbk
+ if self.record_type is not None and self.record_type != RECORD_TYPE.REGION:
+ query_ids = [record._db_id for record in self.working_query_records]
+ ref_ids = [record._db_id for record in self.working_ref_records]
+
+ if DB.metadata is None:
+ raise RuntimeError("DB.metadata is None")
+
+ rec_table = DB.metadata.tables["bgc_record"]
+
+ # contruct two tables that hold the gbk id and the number of subrecords
+ # present in the set of query and ref records respectively
+ query_gbk = (
+ select(
+ rec_table.c.gbk_id,
+ func.count(rec_table.c.gbk_id).label("query_count"),
+ )
+ .where(rec_table.c.id.in_(query_ids))
+ .group_by(rec_table.c.gbk_id)
+ .subquery()
+ )
+
+ ref_gbk = (
+ select(
+ rec_table.c.gbk_id,
+ func.count(rec_table.c.gbk_id).label("ref_count"),
+ )
+ .where(rec_table.c.id.in_(ref_ids))
+ .group_by(rec_table.c.gbk_id)
+ .subquery()
+ )
+
+ # now we can join the two tables and obtain the number of links between
+ # records from the same gbks by multiplying their counts
+ same_gbk_query = select(
+ func.sum(query_gbk.c.query_count * ref_gbk.c.ref_count)
+ ).join(ref_gbk, query_gbk.c.gbk_id == ref_gbk.c.gbk_id)
+
+ same_gbks = DB.execute(same_gbk_query).scalar_one()
+ if same_gbks:
+ num_pairs -= same_gbks
+
return num_pairs
def add_records(self, record_list: list[BGCRecord]) -> None:
diff --git a/big_scape/distances/query.py b/big_scape/distances/query.py
index f2aaff56..eb6c31b9 100644
--- a/big_scape/distances/query.py
+++ b/big_scape/distances/query.py
@@ -43,7 +43,9 @@ def calculate_distances_query(
max_cutoff = max(run["gcf_cutoffs"])
edge_param_id = bs_comparison.get_edge_param_id(run, weights)
- query_bin = bs_comparison.QueryRecordPairGenerator("Query", edge_param_id, weights)
+ query_bin = bs_comparison.QueryRecordPairGenerator(
+ "Query", edge_param_id, weights, run["record_type"]
+ )
query_bin.add_records(query_records)
missing_query_bin = bs_comparison.QueryMissingRecordPairGenerator(query_bin)
@@ -54,9 +56,13 @@ def calculate_distances_query(
query_connected_component = next(
bs_network.get_connected_components(
- max_cutoff, edge_param_id, query_bin, run["run_id"]
- )
+ max_cutoff, edge_param_id, query_bin, run["run_id"], query_record
+ ),
+ None,
)
+ if query_connected_component is None:
+ # no nodes are connected even with the highest cutoffs in the run
+ return query_bin
query_nodes = bs_network.get_nodes_from_cc(query_connected_component, query_records)
@@ -159,47 +165,56 @@ def calculate_distances(run: dict, bin: bs_comparison.RecordPairGenerator):
# fetches the current number of singleton ref <-> connected ref pairs from the database
num_pairs = bin.num_pairs()
- # if there are no more singleton ref <-> connected ref pairs, then break and exit
- if num_pairs == 0:
- break
-
- logging.info("Calculating distances for %d pairs", num_pairs)
+ if num_pairs > 0:
+ logging.info("Calculating distances for %d pairs", num_pairs)
- save_batch = []
- num_edges = 0
+ save_batch = []
+ num_edges = 0
- with tqdm.tqdm(total=num_pairs, unit="edge", desc="Calculating distances") as t:
+ with tqdm.tqdm(
+ total=num_pairs, unit="edge", desc="Calculating distances"
+ ) as t:
- def callback(edges):
- nonlocal num_edges
- nonlocal save_batch
- batch_size = run["cores"] * 100000
- for edge in edges:
- num_edges += 1
- t.update(1)
- save_batch.append(edge)
- if len(save_batch) > batch_size:
- bs_comparison.save_edges_to_db(save_batch, commit=True)
- save_batch = []
+ def callback(edges):
+ nonlocal num_edges
+ nonlocal save_batch
+ batch_size = run["cores"] * 100000
+ for edge in edges:
+ num_edges += 1
+ t.update(1)
+ save_batch.append(edge)
+ if len(save_batch) > batch_size:
+ bs_comparison.save_edges_to_db(save_batch, commit=True)
+ save_batch = []
- bs_comparison.generate_edges(
- bin,
- run["alignment_mode"],
- run["extend_strategy"],
- run["cores"],
- run["cores"] * 2,
- callback,
- )
+ bs_comparison.generate_edges(
+ bin,
+ run["alignment_mode"],
+ run["extend_strategy"],
+ run["cores"],
+ run["cores"] * 2,
+ callback,
+ )
- bs_comparison.save_edges_to_db(save_batch)
+ bs_comparison.save_edges_to_db(save_batch)
- bs_data.DB.commit()
+ bs_data.DB.commit()
- logging.info("Generated %d edges", num_edges)
+ logging.info("Generated %d edges", num_edges)
- if run["skip_propagation"]:
+ if not run["propagate"]:
# in this case we only want one iteration, the Query -> Ref edges
break
+ if isinstance(bin, bs_comparison.MissingRecordPairGenerator):
+ # in this case we only need edges within one cc, no cycles needed
+ break
+
if isinstance(bin, bs_comparison.QueryMissingRecordPairGenerator):
+ # use the num_pairs from the parent bin because in a partial database,
+ # all distances for the first cycle(s) might already be present.
+ # we still only want to stop when no other connected nodes are discovered.
+ if bin.bin.num_pairs() == 0:
+ break
+
bin.cycle_records(max(run["gcf_cutoffs"]))
diff --git a/big_scape/file_input/load_files.py b/big_scape/file_input/load_files.py
index fddf08e2..bd2b17eb 100644
--- a/big_scape/file_input/load_files.py
+++ b/big_scape/file_input/load_files.py
@@ -409,21 +409,16 @@ def get_all_bgc_records_query(
"""Get all BGC records from the working list of GBKs
Args:
- gbks (list[GBK]): list of GBK objects
run (dict): run parameters
+ gbks (list[GBK]): list of GBK objects
Returns:
- list[bs_gbk.BGCRecord]: list of BGC records
+ list[bs_gbk.BGCRecord], bs_gbk.BGCRecord: list of BGC records, query BGC record
"""
all_bgc_records: list[bs_gbk.BGCRecord] = []
for gbk in gbks:
if gbk.region is not None:
- gbk_records = bs_gbk.bgc_record.get_sub_records(
- gbk.region, run["record_type"]
- )
if gbk.source_type == bs_enums.SOURCE_TYPE.QUERY:
- query_record_type = run["record_type"]
-
query_record_type = run["record_type"]
query_record_number = run["query_record_number"]
@@ -435,15 +430,24 @@ def get_all_bgc_records_query(
query_record = query_sub_records[0]
else:
- query_record = [
+ matching_query_records = [
record
for record in query_sub_records
if record.number == query_record_number
- ][0]
+ ]
+ if len(matching_query_records) == 0:
+ raise RuntimeError(
+ f"Could not find {query_record_type.value} number {query_record_number} in query GBK. "
+ "Depending on config settings, overlapping records will be merged and take on the lower number."
+ )
+ query_record = matching_query_records[0]
all_bgc_records.append(query_record)
else:
+ gbk_records = bs_gbk.bgc_record.get_sub_records(
+ gbk.region, run["record_type"]
+ )
all_bgc_records.extend(gbk_records)
return all_bgc_records, query_record
diff --git a/big_scape/network/families.py b/big_scape/network/families.py
index bf07f71a..e5974d08 100644
--- a/big_scape/network/families.py
+++ b/big_scape/network/families.py
@@ -370,28 +370,18 @@ def run_family_assignments_query(
# get_connected_components returns a list of connected components, but we only
# want the first one, so we use next()
- try:
- query_connected_component = next(
- bs_network.get_connected_components(
- cutoff, query_bin.edge_param_id, query_bin, run["run_id"]
- )
- )
-
- cc_cutoff[cutoff] = query_connected_component
-
- logging.debug(
- "Found connected component with %d edges",
- len(query_connected_component),
- )
-
- regions_families = generate_families(
- query_connected_component, query_bin.label, cutoff, run["run_id"]
- )
-
- # save families to database
- save_to_db(regions_families)
+ query_connected_component = next(
+ bs_network.get_connected_components(
+ cutoff,
+ query_bin.edge_param_id,
+ query_bin,
+ run["run_id"],
+ query_record,
+ ),
+ None,
+ )
- except StopIteration:
+ if query_connected_component is None:
logging.warning(
"No connected components found for %s bin at cutoff %s",
query_bin.label,
@@ -399,6 +389,20 @@ def run_family_assignments_query(
)
continue
+ cc_cutoff[cutoff] = query_connected_component
+
+ logging.debug(
+ "Found connected component with %d edges",
+ len(query_connected_component),
+ )
+
+ regions_families = generate_families(
+ query_connected_component, query_bin.label, cutoff, run["run_id"]
+ )
+
+ # save families to database
+ save_to_db(regions_families)
+
DB.commit()
# no connected components found
diff --git a/big_scape/network/network.py b/big_scape/network/network.py
index d228a379..0bfad3bb 100644
--- a/big_scape/network/network.py
+++ b/big_scape/network/network.py
@@ -32,6 +32,7 @@ def get_connected_components(
edge_param_id: int,
bin: bs_comparison.RecordPairGenerator,
run_id: int,
+ seed_record: Optional[BGCRecord] = None,
) -> Generator[list[tuple[int, int, float, float, float, float, int]], None, None]:
"""Generate a network for each connected component in the network
If a seed record is given, the connected component will be generated starting from that record
@@ -54,7 +55,7 @@ def get_connected_components(
# generate connected components using dfs
generate_connected_components(
- cutoff, edge_param_id, bin.label, run_id, include_record_table
+ cutoff, edge_param_id, bin.label, run_id, include_record_table, seed_record
)
cc_ids = get_connected_component_ids(
diff --git a/big_scape/output/html_template/output/html_content/css/style.css b/big_scape/output/html_template/output/html_content/css/style.css
index 69db78e9..72d3d7ec 100644
--- a/big_scape/output/html_template/output/html_content/css/style.css
+++ b/big_scape/output/html_template/output/html_content/css/style.css
@@ -24,7 +24,6 @@ html[data-theme='dark'] {
--overview-button-background: hsl(var(--hue), 34%, 48%);
--button-text-color: hsl(var(--hue), 10%, 10%);
--background-color: hsl(var(--hue), 20%, 12%);
- /* --background-header: rgba(159, 159, 143, 0.188); */
--background-header: hsl(var(--hue), 15%, 20%);
--li-selected-color: hsl(var(--hue), 70%, 60%);
--row-selected-color: hsl(var(--hue), 60%, 70%)
@@ -160,6 +159,7 @@ a.anchor {
color: var(--text-color-normal);
background-color: var(--background-color);
overflow: scroll;
+ opacity: 90%;
}
.desc-container.active {
diff --git a/big_scape/output/html_template/output/html_content/js/bigscape.js b/big_scape/output/html_template/output/html_content/js/bigscape.js
index d3f5f91c..767641fa 100755
--- a/big_scape/output/html_template/output/html_content/js/bigscape.js
+++ b/big_scape/output/html_template/output/html_content/js/bigscape.js
@@ -360,11 +360,9 @@ function Bigscape(run_data, bs_data, bs_families, bs_alignment, bs_similarity, n
var ui = Viva.Graph.svg('circle')
.attr('r', 10)
.attr('fill', (fam_colors[bs_to_cl[node.id]]));
- if (run_data["mode"] == "Cluster") {
- if (bs_data[node.id]["source"] == "mibig" || bs_data[node.id]["source"] == "reference") {
- ui.attr("stroke", "blue");
- ui.attr("stroke-width", "4px");
- }
+ if (bs_data[node.id]["source"] == "mibig" || bs_data[node.id]["source"] == "reference") {
+ ui.attr("stroke", "blue");
+ ui.attr("stroke-width", "4px");
}
if (run_data["mode"] == "Query") {
if (bs_data[node.id]["source"] == "query") {
diff --git a/big_scape/output/html_template/output/index.html b/big_scape/output/html_template/output/index.html
index 37694256..33d5aeeb 100644
--- a/big_scape/output/html_template/output/index.html
+++ b/big_scape/output/html_template/output/index.html
@@ -228,8 +228,8 @@ Network
Filter the connected components table. All filters allow for comma separated input that will
be handled as logical OR operators.
- Fuzzy search organism names, e.g. "Streptomyces"
+ Fuzzy search GBK descriptions, e.g. "Streptomyces"
Network
$("#cc-table-filters").toggleClass("hidden")
})
$("#clear-filters").on("click", (event) => {
- $("#organism-filter").val("")
+ $("#desc-filter").val("")
$("#bgc-filter").val("")
$("#domain-filter").val("")
$("#family-filter").val("")
@@ -558,7 +558,7 @@ Network
run_params["cutoff"] = cutoff
var bin_label = $("#network-selection option:selected").text()
- var org_filter = $("#organism-filter").val().toString().trim()
+ var org_filter = $("#desc-filter").val().toString().trim()
var pf_filter = $("#domain-filter").val().toString().trim()
var fam_filter = $("#family-filter").val().toString().trim()
var bgc_filter = $("#bgc-filter").val().toString().trim()
@@ -573,7 +573,7 @@ Network
AND connected_component.bin_label=="${bin_label}"`
if (org_filter) {
- var conditions = org_filter.split(",").map(org => `gbk.organism LIKE "%${org.trim()}%"`)
+ var conditions = org_filter.split(",").map(org => `gbk.description LIKE "%${org.trim()}%"`)
cc_query += ` AND (${conditions.join(" OR ")})`
}
if (pf_filter) {
@@ -647,7 +647,7 @@ Network
}
var tsv_text = `# Collection of selected connected components
# Run info: ${run_data["label"]} ${run_data["cutoff"]} ${$("#network-selection option:selected").text()}
-# Organism filter: ${$("#organism-filter").val()}
+# Description filter: ${$("#desc-filter").val()}
# BGC filter: ${$("#bgc-filter").val()}
# Pfam filter: ${$("#domain-filter").val()}
# Family filter: ${$("#family-filter").val()}\n
@@ -672,7 +672,7 @@ Network
if (!dom_data.hasOwnProperty(cds_id)) {
dom_data[cds_id] = []
}
- dom_data[cds_id].push({ "code": domains[i][1], "start": domains[i][2], "end": domains[i][3], "bitscore": domains[i][4] })
+ dom_data[cds_id].push({ "code": domains[i][1], "start": domains[i][2], "end": domains[i][3], "bitscore": domains[i][4].toFixed(3) })
}
return dom_data
}
@@ -693,7 +693,7 @@ Network
return cds_data
}
function generate_bs_data(record_ids, run_data) {
- var records_query = `SELECT gbk.id, gbk.organism, length(gbk.nt_seq), gbk.hash, gbk.path,
+ var records_query = `SELECT gbk.id, gbk.description, length(gbk.nt_seq), gbk.hash, gbk.path,
bgc_record.record_type, bgc_record.nt_start, bgc_record.nt_stop,
bgc_record.record_number, bgc_record.id FROM bgc_record
INNER JOIN gbk ON bgc_record.gbk_id==gbk.id
@@ -733,17 +733,17 @@ Network
}
new_row["record_start"] = rec_start
new_row["record_stop"] = rec_stop
+
+ if (gbk_path.indexOf(run_data["reference_dir"]) > -1) {
+ new_row["source"] = "reference"
+ }
+ if (gbk_path.indexOf(`mibig_antismash_${run_data["mibig_version"]}_gbk`) > -1) {
+ new_row["source"] = "mibig"
+ }
if (run_data["mode"] == "Query") {
if (filename == run_data["query_path"]) {
new_row["source"] = "query"
}
- } else {
- if (gbk_path.indexOf(run_data["reference_dir"]) > -1) {
- new_row["source"] = "reference"
- }
- if (gbk_path.indexOf(run_data["mibig_version"]) > -1) {
- new_row["source"] = "mibig"
- }
}
bs_data[record_id] = new_row
}
diff --git a/test/comparison/test_binning.py b/test/comparison/test_binning.py
index 730f8e31..ec62e475 100644
--- a/test/comparison/test_binning.py
+++ b/test/comparison/test_binning.py
@@ -161,7 +161,7 @@ def test_num_pairs_correct_with_query_ref(self):
for bgc in bgc_list:
bgc.save_record("Region")
- new_bin = QueryRecordPairGenerator("test", 1, "mix")
+ new_bin = QueryRecordPairGenerator("test", 1, "mix", None)
new_bin.add_records(bgc_list)
@@ -290,7 +290,7 @@ def test_query_to_ref_pair_generator(self):
create_mock_gbk(i, bs_enums.SOURCE_TYPE.REFERENCE) for i in range(1, 4)
]
- query_to_ref_pair_generator = QueryRecordPairGenerator("mix", 1, "mix")
+ query_to_ref_pair_generator = QueryRecordPairGenerator("mix", 1, "mix", None)
source_records = [query_gbk.region]
for ref_gbk in ref_gbks:
diff --git a/test/integration/test_comparison.py b/test/integration/test_comparison.py
index c81c5e74..7ea0b6c1 100644
--- a/test/integration/test_comparison.py
+++ b/test/integration/test_comparison.py
@@ -1020,7 +1020,9 @@ def test_missing_query_pair_generator_first_iteration(self):
create_mock_gbk(i, bs_enums.SOURCE_TYPE.REFERENCE) for i in range(1, 5)
]
- query_pair_generator = bs_comparison.QueryRecordPairGenerator("mix", 1, "mix")
+ query_pair_generator = bs_comparison.QueryRecordPairGenerator(
+ "mix", 1, "mix", None
+ )
source_records = [query_gbk.region]
for ref_gbk in ref_gbks:
source_records.append(ref_gbk.region)
@@ -1147,7 +1149,9 @@ def test_query_generators_workflow(self):
create_mock_gbk(i, bs_enums.SOURCE_TYPE.REFERENCE) for i in range(1, 5)
]
- query_pair_generator = bs_comparison.QueryRecordPairGenerator("mix", 1, "mix")
+ query_pair_generator = bs_comparison.QueryRecordPairGenerator(
+ "mix", 1, "mix", None
+ )
source_records = [query_gbk.region]
for ref_gbk in ref_gbks:
source_records.append(ref_gbk.region)
@@ -1467,7 +1471,7 @@ def test_generate_bins_query_workflow(self):
"record_type": bs_enums.RECORD_TYPE.REGION,
"cores": 1,
"classify": bs_enums.CLASSIFY_MODE.CLASS,
- "skip_propagation": False,
+ "propagate": True,
"gcf_cutoffs": [0.1, 0.7],
}
@@ -1488,7 +1492,7 @@ def test_generate_bins_query_workflow(self):
# generate initial query -> ref pairs
query_bin = bs_comparison.QueryRecordPairGenerator(
- "Query", edge_param_id, weights
+ "Query", edge_param_id, weights, run["record_type"]
)
query_bin.add_records(query_records)
@@ -1603,14 +1607,16 @@ def test_calculate_distances_query(self):
"record_type": bs_enums.RECORD_TYPE.REGION,
"cores": 1,
"classify": bs_enums.CLASSIFY_MODE.CLASS,
- "skip_propagation": False,
+ "propagate": True,
"run_id": 1,
"gcf_cutoffs": [0.1, 0.8],
}
query_record, list_bgc_records = create_mock_query_dataset(run)
- query_to_ref_bin = bs_comparison.QueryRecordPairGenerator("Query_Ref", 1, "mix")
+ query_to_ref_bin = bs_comparison.QueryRecordPairGenerator(
+ "Query_Ref", 1, "mix", run["record_type"]
+ )
query_records = bs_query.get_query_records(run, list_bgc_records, query_record)
query_to_ref_bin.add_records(query_records)