Function get_data has a Cognitive Complexity of 67 (exceeds 5 allowed). Consider refactoring.

Open

    def get_data(self, disease_data):

        disease_annots = {}
        list_to_yield = []

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Function get_data has a Cognitive Complexity of 43 (exceeds 5 allowed). Consider refactoring.

Open

    def get_data(self, gene_data, batch_size, test_set):

        gene_dataset = {}
        list_to_yield = []

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Function render has 108 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  render() {
    const filteredData = this.props.data.filter((dat) => this.filterCallback(dat));
    const all_methods = this.props.data[0].predictionMethodsMatched.concat(
      this.props.data[0].predictionMethodsNotCalled,
      this.props.data[0].predictionMethodsNotMatched

Function get_data has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.

Open

    def get_data():
        path = "tmp";
        S3File("mod-datadumps", "disease-ontology.obo", path).download()
        do_data = TXTFile(path + "/disease-ontology.obo").get_data()

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File mapping_schema.py has 340 lines of code (exceeds 250 allowed). Consider refactoring.

Open

mapping_schema = {
    "settings": {
        "index": {
            "max_result_window": 15000,
            "analysis": {

Function get_data has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

    def get_data():
        path = "tmp";
        S3File("mod-datadumps/data", "so.obo", path).download()
        so_data = TXTFile(path + "/so.obo").get_data()

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File search_helper.py has 282 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import json


def build_es_aggregation_body_request(es_query, category, category_filters):
    agg_query_body = {

Function get_data has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    def get_data(self):
        omim_dataset = {}

        for row in self.omim_data:
            if len(row) < 3:

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Function render has 64 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  render() {
    const speciesPresent = this.props.data.map((orthData) => {
      return orthData.gene2SpeciesName;
    });
    // refine the species order to keep only species present in orthologs

Function get_data has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def get_data(mod_name, test_set, gene_master_dict):
        path = "tmp"
        filename = None
        filename_comp = None
        if test_set == True:

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Function render has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

  render() {
    if (this.props.loading) {
      return <span>loading...</span>;
    }

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Function render has 56 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  render() {
    if (this.props.loading) {
      return <span>loading...</span>;
    }

Function MethodCell has 52 lines of code (exceeds 25 allowed). Consider refactoring.

Open

const MethodCell = (props) => {
  const {
    predictionMethodsMatched,
    predictionMethodsNotMatched
  } = props;

Function load_from_mods has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

    def load_from_mods(self, test_set):
        mods = [RGD(), MGI(), ZFIN(), SGD(), WormBase(), FlyBase(), Human()]


        gene_master_dict = {} # Build a dictionary of sets for all indexed MODs/genes. Used for filtering orthology.

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Function render has 45 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  render() {
    let currentRoute=this.props.location.pathname.replace('/','');
    currentRoute= currentRoute==''?'home' : currentRoute;

    return (

Function parseGOOBO has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

def parseGOOBO(filename):
    """
    Parses a Gene Ontology dump in OBO v1.2 format.
    Yields each 
    Keyword arguments:

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Function format_aggregation_results has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

def format_aggregation_results(aggregation_results, category, category_filters):
    if category == '':
        category_obj = {
            'values': [],
            'key': 'category'

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Function get_complete_url has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def get_complete_url (self, local_id, global_id):

        complete_url = None

        if 'MGI' in global_id:

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Function attach_homolog_data has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

    def attach_homolog_data(self, genes):

        for row in self.homolog_data:

            gene_1 = self._process_gene_id_from_panther(row[0], genes)

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Function render has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  render() {
    const diseases = this.props.data;
    const filename = this.props.filename;

    // the way the incoming data is grouped doesn't exactly align with the way