Avoid deeply nested control flow statements.

Open

                        if ( attrs[ i ] ) {
                            name = attrs[ i ].name;
                            if ( name.indexOf( "data-" ) === 0 ) {
                                name = camelCase( name.slice( 5 ) );
                                dataAttr( elem, name, data[ name ] );

Avoid deeply nested control flow statements.

Open

                    if ( conv && s.throws ) {
                        response = conv( response );
                    } else {
                        try {
                            response = conv( response );

Function on has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

function on( elem, types, selector, data, fn, one ) {

Avoid deeply nested control flow statements.

Open

                    if ( copyIsArray && !Array.isArray( src ) ) {
                        clone = [];
                    } else if ( !copyIsArray && !jQuery.isPlainObject( src ) ) {
                        clone = {};
                    } else {

Avoid deeply nested control flow statements.

Open

                        for ( type in data.events ) {
                            if ( special[ type ] ) {
                                jQuery.event.remove( elem, type );

                            // This is a shortcut to avoid jQuery.event.remove's overhead

Avoid deeply nested control flow statements.

Open

                    if ( hasScripts ) {

                        // Support: Android <=4.0 only, PhantomJS 1 only
                        // push.apply(_, arraylike) throws on ancient WebKit
                        jQuery.merge( scripts, getAll( node, "script" ) );

Avoid deeply nested control flow statements.

Open

                    if ( newContext !== context || !support.scope ) {

                        // Capture the context ID, setting it first if necessary
                        if ( ( nid = context.getAttribute( "id" ) ) ) {
                            nid = nid.replace( rcssescape, fcssescape );

Avoid deeply nested control flow statements.

Open

                    if ( !selector ) {
                        push.apply( results, seed );
                        return results;
                    }

Avoid deeply nested control flow statements.

Open

                    if ( restoreDisplay == null ) {
                        display = style.display;
                        restoreDisplay = display === "none" ? "" : display;
                    }

Avoid deeply nested control flow statements.

Open

                        if entity_type == "Gene":
                            self.make_pharmgkb_gene_node(
                                fh=node,
                                this_id=entity_id,
                                name=entity_name,

Avoid deeply nested control flow statements.

Open

                        if protein in string_to_uniprot_id_map:
                            uniprot_curie = (
                                f"UniProtKB:{string_to_uniprot_id_map[protein]}"
                            )
                            uniprot_curie = collapse_uniprot_curie(uniprot_curie)

Avoid deeply nested control flow statements.

Open

                if cur_gene_name in linec_split:
                    #print("found")
                    found = 1
                    countORFs = countORFs + 1

Avoid deeply nested control flow statements.

Open

                        if not item:
                            continue  # not xrefs, skip
                        item = item.strip('"')  # remove quotes around each item

Function result_dict_to_tsv has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def result_dict_to_tsv(result_dict: dict, outfile: str) -> None:
    """Convert a result_dict to a TSV for output."""
    with open(outfile, "wt") as f:
        # header
        f.write("\t".join(result_dict["head"]["vars"]) + "\n")

• Read up
  Read up

Function transform has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def transform(
    input_dir: str, output_dir: str, sources: Optional[List[str]] = None
) -> None:
    """Call scripts in kg_covid_19/transform/[source name]/ to transform data.

• Read up
  Read up

Avoid deeply nested control flow statements.

Open

                        if self.key_parsed_ids not in dat:
                            dat[self.key_parsed_ids] = dict()
                        dat[self.key_parsed_ids][key] = value

Avoid deeply nested control flow statements.

Open

                        for x in v:
                            r = self.parse_doc_fields(x, allowed_properties, remap)
                            for k2, v2 in r.items():
                                update_properties(k2, v2)
            else:

Function make_id_mapping_file has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def make_id_mapping_file(

Avoid deeply nested control flow statements.

Open

                        if gene not in seen_genes:
                            seen_genes.add(gene)
                            ensemble_gene = f"ENSEMBL:{gene}"
                            gene_informations = self.gene_info_map[
                                self.ensembl2ncbi_map[gene]

Function elastic_search_query has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def elastic_search_query(