Function get_current_index has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def get_current_index(self):
        current = self.es.indices.get(self.es_index, ignore=[400, 404])
        if "status" in current and current["status"] == 404:
            current = None
            current_name = None

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

Open

def build_es_search_body_request(query, category, es_query, json_response_fields, search_fields, sort_by):

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

Open

    def index_data(self, data, data_type, op_type):
        s = time.time()
        bulk_data = []
        id_to_use = None

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Avoid deeply nested control flow statements.

Open

                        if value.split(" ")[-2] == "EXACT":
                            value = (" ".join(value.split(" ")[:-2]))[1:-1]
                        else:
                            continue
                    if key == "def":

Avoid deeply nested control flow statements.

Open

                        if value.split(" ")[-2] == "EXACT":
                            value = (" ".join(value.split(" ")[:-2]))[1:-1]
                        else:
                            continue
                    if key == "def":

Avoid deeply nested control flow statements.

Open

                        if pubMedId is not None:
                            if ':' in pubMedId:
                                localPubMedId = pubMedId.split(":")[1]
                        publicationModId = pub.get('modPublicationId')

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

Open

    def get_species(self, taxon_id):
        if taxon_id in ("NCBITaxon:7955"):
            return "Danio rerio"
        elif taxon_id in ("NCBITaxon:6239"):
            return "Caenorhabditis elegans"

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

Open

    def search(self, query, limit, offset, category, sort_by, params):

Avoid deeply nested control flow statements.

Open

                        if publicationModId is not None:
                            localPubModId = publicationModId.split(":")[1]
                        if pubMedId is not None:

Avoid deeply nested control flow statements.

Open

                        if pubMedId is not None:
                            pubs.append({'pubMedId': pubMedId, 'pubMedUrl': 'https://www.ncbi.nlm.nih.gov/pubmed/' + localPubMedId})
                        else:
                            if publicationModId is not None:
                                pubs.append({'publicationModId': publicationModId, 'pubModUrl': self.get_complete_pub_url(localPubModId, publicationModId)})

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

Open

    def add_disease_annotation_to_gene(self, gene_id, omim_id, species):
        if omim_id not in self.omim_dataset or gene_id not in self.genes:
            return

        gene_symbol = self.genes[gene_id]["symbol"].upper()

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

Open

def filter_highlighting(highlight):
    if highlight is None:
        return None

    for k in highlight.keys():

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Function build_search_query has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

def build_search_query(query, search_fields, category, category_filters, args):

Function _process_gene_id_from_panther has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def _process_gene_id_from_panther(self, gene_ids_panther, genes):
        gene_ids = gene_ids_panther.split("|")

        if gene_ids[0] in self.organism_to_mods:
            mod = self.organism_to_mods[gene_ids[0]]

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Function searchReducer has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

const searchReducer = function (state = DEFAULT_STATE, action) {
  // TODO cleanup fromJS/toJS handling here.
  switch(action.type) {
  case 'SEARCH_ERROR':
    if (!action.payload) {

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Function build_search_query has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def build_search_query(query, search_fields, category, category_filters, args):
    es_query = build_search_params(query, search_fields)

    if category == '':
        return es_query

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Function build_es_search_body_request has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def build_es_search_body_request(query, category, es_query, json_response_fields, search_fields, sort_by):
    es_search_body = {
        '_source': json_response_fields,
        'highlight': {
            'fields': {}

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Function load_go has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def load_go(self):
        path = "tmp"
        S3File("mod-datadumps/GO/ANNOT", "gene_association.human.gz", path).download()
        go_annot_dict = {}
        with gzip.open(path + "/gene_association.human.gz", 'rb') as file:

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Function attach_annotations has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def attach_annotations(self, genes):
        for annot in self.annots:
            go_id = annot['go_id']
            gene_id = annot['gene_id']

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Function build_search_params has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def build_search_params(query, search_fields):
    if query is "":
        es_query = {"match_all": {}}
    else:
        es_query = {'bool':

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