Fix some more code

src/chanjo2/crud/intervals.py

@@ -180,28 +180,22 @@ def get_ensembl_gene_ids_from_gene_filter(filter_value, filter_column):
         genes = (
             db.query(SQLGene.ensembl_ids).filter(filter_column.in_(filter_value)).all()
         )
-        return [gene.ensembl_ids for gene in genes]
+        return [ensembl_id for gene in genes for ensembl_id in gene.ensembl_ids]
 
     # Handle filtering based on ensembl_ids, ensembl_gene_ids, hgnc_ids, or hgnc_symbols
     if ensembl_ids:
         intervals = intervals.filter(
             func.json_contains(SQLGene.ensembl_ids, func.json_array(*ensembl_ids))
         )
-    elif ensembl_gene_ids:
-        intervals = intervals.filter(
-            interval_type.ensembl_gene_id.in_(ensembl_gene_ids)
-        )
     elif hgnc_ids:
         ensembl_gene_ids = get_ensembl_gene_ids_from_gene_filter(
             hgnc_ids, SQLGene.hgnc_id
         )
-        intervals = intervals.filter(
-            interval_type.ensembl_gene_id.in_(ensembl_gene_ids)
-        )
     elif hgnc_symbols:
         ensembl_gene_ids = get_ensembl_gene_ids_from_gene_filter(
             hgnc_symbols, SQLGene.hgnc_symbol
         )
+    if ensembl_gene_ids:
         intervals = intervals.filter(
             interval_type.ensembl_gene_id.in_(ensembl_gene_ids)
         )

src/chanjo2/meta/handle_load_intervals.py

@@ -43,9 +43,13 @@ def read_resource_lines(build: Builds, interval_type: IntervalType) -> Iterator[
     return response.iter_lines(decode_unicode=True)
 
 
-def _replace_empty_cols(line: str) -> List[Union[str, None]]:
+def _replace_empty_cols(line: str, nr_expected_columns: int) -> List[Union[str, None]]:
     """Split line into columns, replacing empty columns with None values."""
-    return [None if cell == "" else cell for cell in line.split("\t")]
+    cols = [None if cell == "" else cell for cell in line.split("\t")]
+
+    # Make sure that expected nr of cols are returned if last cols are blank
+    cols += [None] * (nr_expected_columns - len(cols))
+    return cols
 
 
 async def update_genes(
@@ -93,7 +97,7 @@ def update_or_insert_gene(session, sql_gene):
         if line == END_OF_PARSED_FILE:
             break
 
-        items: List = _replace_empty_cols(line=line)
+        items: List = _replace_empty_cols(line=line, nr_expected_columns=len(header))
 
         try:
             sql_gene = SQLGene(
@@ -151,7 +155,9 @@ async def update_transcripts(
         if line == END_OF_PARSED_FILE:
             break
 
-        items: List = _replace_empty_cols(line=line)
+        items: List = _replace_empty_cols(line=line, nr_expected_columns=len(header))
+        LOG.warning(header)
+        LOG.warning(items)
 
         try:
             transcript = TranscriptBase(
@@ -216,7 +222,7 @@ async def update_exons(
         if line == END_OF_PARSED_FILE:
             break
 
-        items: List = _replace_empty_cols(line=line)
+        items: List = _replace_empty_cols(line=line, nr_expected_columns=len(header))
 
         try:
             # Load Exon interval into the database