path: root/gn2/wqflask/show_trait/show_trait.py

from typing import Dict

import string
import datetime
import uuid
import requests
import json as json

from collections import OrderedDict

import numpy as np
import scipy.stats as ss

from gn2.wqflask.database import database_connection

from gn2.base import webqtlConfig
from gn2.wqflask.show_trait.SampleList import SampleList
from gn2.base.trait import create_trait
from gn2.base import data_set
from gn2.utility import helper_functions
from gn2.utility.tools import get_setting, locate_ignore_error
from gn2.utility.tools import GN_PROXY_URL
from gn2.utility.redis_tools import get_redis_conn, get_resource_id

from gn3.authentication import get_highest_user_access_role

Redis = get_redis_conn()
ONE_YEAR = 60 * 60 * 24 * 365


###############################################
#
# Todo: Put in security to ensure that user has permission to access
# confidential data sets And add i.p.limiting as necessary
#
##############################################


class ShowTrait:
    def __init__(self, db_cursor, user_id, kw):
        if 'trait_id' in kw and kw['dataset'] != "Temp":
            self.temp_trait = False
            self.trait_id = kw['trait_id']
            helper_functions.get_species_dataset_trait(self, kw)
            self.resource_id = get_resource_id(self.dataset,
                                           self.trait_id)
        elif 'group' in kw:
            self.temp_trait = True
            self.trait_id = "Temp_" + kw['species'] + "_" + kw['group'] + \
                "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
            self.temp_species = kw['species']
            self.temp_group = kw['group']
            self.dataset = data_set.create_dataset(
                dataset_name="Temp", dataset_type="Temp", group_name=self.temp_group)

            # Put values in Redis so they can be looked up later if
            # added to a collection
            Redis.set(self.trait_id, kw['trait_paste'], ex=ONE_YEAR)
            self.trait_vals = kw['trait_paste'].split()
            self.this_trait = create_trait(dataset=self.dataset,
                                           name=self.trait_id,
                                           cellid=None)
        else:
            self.temp_trait = True
            self.trait_id = kw['trait_id']
            self.temp_species = self.trait_id.split("_")[1]
            self.temp_group = self.trait_id.split("_")[2]
            self.dataset = data_set.create_dataset(
                dataset_name="Temp", dataset_type="Temp", group_name=self.temp_group)
            self.this_trait = create_trait(dataset=self.dataset,
                                           name=self.trait_id,
                                           cellid=None)
            self.trait_vals = Redis.get(self.trait_id).split()

        # Get verify/rna-seq link URLs
        try:
            blatsequence = self.this_trait.blatseq if self.dataset.type == "ProbeSet" else self.this_trait.sequence
            if not blatsequence:
                # XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
                seqs = ()
                if self.dataset.type == "ProbeSet":
                    db_cursor.execute(
                        "SELECT Probe.Sequence, Probe.Name "
                        "FROM Probe, ProbeSet, ProbeSetFreeze, "
                        "ProbeSetXRef WHERE "
                        "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
                        "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
                        "ProbeSetFreeze.Name = %s AND "
                        "ProbeSet.Name = %s AND "
                        "Probe.ProbeSetId = ProbeSet.Id ORDER "
                        "BY Probe.SerialOrder",
                        (self.this_trait.dataset.name, self.this_trait.name,)
                    )
                else:
                    db_cursor.execute(
                        "SELECT Geno.Sequence "
                        "FROM Geno, GenoXRef, GenoFreeze "
                        "WHERE Geno.Name = %s AND "
                        "Geno.Id = GenoXRef.GenoId AND "
                        "GenoXRef.GenoFreezeId = GenoFreeze.Id AND "
                        "GenoFreeze.Name = %s",
                        (self.this_trait.name, self.this_trait.dataset.name)
                    )
                seqs = db_cursor.fetchall()
                if not seqs:
                    raise ValueError
                else:
                    blatsequence = ''
                    for seqt in seqs:
                        if int(seqt[1][-1]) % 2 == 1:
                            blatsequence += string.strip(seqt[0])

            # --------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe
            blatsequence = '%3E' + self.this_trait.name + '%0A' + blatsequence + '%0A'

            # XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
            seqs = ()
            db_cursor.execute(
                "SELECT Probe.Sequence, Probe.Name "
                "FROM Probe, ProbeSet, ProbeSetFreeze, "
                "ProbeSetXRef WHERE "
                "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
                "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
                "ProbeSetFreeze.Name = %s AND ProbeSet.Name = %s "
                "AND Probe.ProbeSetId = ProbeSet.Id "
                "ORDER BY Probe.SerialOrder",
                (self.this_trait.dataset.name, self.this_trait.name,)
            )
            seqs = db_cursor.fetchall()
            for seqt in seqs:
                if int(seqt[1][-1]) % 2 == 1:
                    blatsequence += '%3EProbe_' + \
                        seqt[1].strip() + '%0A' + seqt[0].strip() + '%0A'

            if self.dataset.group.species == "rat":
                self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % (
                    'rat', 'rn7', blatsequence)
                self.UTHSC_BLAT_URL = ""
            elif self.dataset.group.species == "mouse":
                self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % (
                    'mouse', 'mm10', blatsequence)
                self.UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % (
                    'mouse', 'mm10', blatsequence)
            elif self.dataset.group.species == "human":
                self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % (
                    'human', 'hg38', blatsequence)
                self.UTHSC_BLAT_URL = ""
            else:
                self.UCSC_BLAT_URL = ""
                self.UTHSC_BLAT_URL = ""
        except:
            self.UCSC_BLAT_URL = ""
            self.UTHSC_BLAT_URL = ""

        if self.dataset.type == "ProbeSet":
            self.show_probes = "True"

        trait_units = get_trait_units(self.this_trait)
        self.get_external_links()
        self.build_correlation_tools()

        self.ncbi_summary = get_ncbi_summary(self.this_trait)

        # Get nearest marker for composite mapping
        if not self.temp_trait:
            if check_if_attr_exists(self.this_trait, 'locus_chr') and self.dataset.type != "Geno" and self.dataset.type != "Publish":
                self.nearest_marker = get_nearest_marker(
                    self.this_trait, self.dataset)
            else:
                self.nearest_marker = ""

        self.make_sample_lists()

        trait_vals_by_group = []
        for sample_type in self.sample_groups:
            trait_vals_by_group.append(get_trait_vals(sample_type.sample_list))

        self.max_digits_by_group, self.no_decimal_place = get_max_digits(trait_vals_by_group)

        self.qnorm_vals = quantile_normalize_vals(self.sample_groups, trait_vals_by_group)
        self.z_scores = get_z_scores(self.sample_groups, trait_vals_by_group)

        self.temp_uuid = uuid.uuid4()

        self.sample_group_types = OrderedDict()
        if len(self.sample_groups) > 1:
            self.sample_group_types['samples_primary'] = self.dataset.group.name
            self.sample_group_types['samples_other'] = "Other"
            self.sample_group_types['samples_all'] = "All"
        else:
            self.sample_group_types['samples_primary'] = self.dataset.group.name
        sample_lists = [group.sample_list for group in self.sample_groups]

        self.categorical_var_list = []
        self.numerical_var_list = []
        if not self.temp_trait:
            # ZS: Only using first samplelist, since I think mapping only uses those samples
            self.categorical_var_list = get_categorical_variables(
                self.this_trait, self.sample_groups[0])
            self.numerical_var_list = get_numerical_variables(
                self.this_trait, self.sample_groups[0])

        # ZS: Get list of chromosomes to select for mapping
        self.chr_list = [["All", -1]]
        for i, this_chr in enumerate(self.dataset.species.chromosomes.chromosomes(db_cursor)):
            self.chr_list.append(
                [self.dataset.species.chromosomes.chromosomes(db_cursor)[this_chr].name, i])

        self.genofiles = self.dataset.group.get_genofiles()
        study_samplelist_json = self.dataset.group.get_study_samplelists()
        self.study_samplelists = [study["title"] for study in study_samplelist_json]

        # ZS: No need to grab scales from .geno file unless it's using
        # a mapping method that reads .geno files
        if "QTLReaper" or "R/qtl" in dataset.group.mapping_names:
            if self.genofiles:
                self.scales_in_geno = get_genotype_scales(self.genofiles)
            else:
                self.scales_in_geno = get_genotype_scales(
                    self.dataset.group.name + ".geno")
        else:
            self.scales_in_geno = {}

        self.has_num_cases = has_num_cases(self.this_trait)

        # ZS: Needed to know whether to display bar chart + get max
        # sample name length in order to set table column width
        self.num_values = 0
        # ZS: So it knows whether to display the Binary R/qtl mapping
        # method, which doesn't work unless all values are 0 or 1
        self.binary = "true"
        # ZS: Since we don't want to show log2 transform option for
        # situations where it doesn't make sense
        self.negative_vals_exist = "false"
        max_samplename_width = 1
        for group in self.sample_groups:
            for sample in group.sample_list:
                if len(sample.name) > max_samplename_width:
                    max_samplename_width = len(sample.name)
                if sample.display_value != "x":
                    self.num_values += 1
                    if sample.display_value != 0 or sample.display_value != 1:
                        self.binary = "false"
                    if sample.value < 0:
                        self.negative_vals_exist = "true"

        # ZS: Check whether any attributes have few enough distinct
        # values to show the "Block samples by group" option
        self.categorical_attr_exists = "false"
        for attribute in self.sample_groups[0].attributes:
            if len(self.sample_groups[0].attributes[attribute].distinct_values) <= 10:
                self.categorical_attr_exists = "true"
                break

        sample_column_width = max_samplename_width * 8

        self.stats_table_width, self.trait_table_width = get_table_widths(
            self.sample_groups, sample_column_width, self.has_num_cases)

        if self.num_values >= 5000:
            self.maf = 0.01
        else:
            self.maf = 0.05

        trait_symbol = None
        short_description = None
        if not self.temp_trait:
            if self.this_trait.symbol:
                trait_symbol = self.this_trait.symbol
                short_description = trait_symbol

            elif hasattr(self.this_trait, 'post_publication_abbreviation'):
                short_description = self.this_trait.post_publication_abbreviation

            elif hasattr(self.this_trait, 'pre_publication_abbreviation'):
                short_description = self.this_trait.pre_publication_abbreviation

        # Todo: Add back in the ones we actually need from below, as we discover we need them
        hddn = OrderedDict()

        if self.dataset.group.allsamples:
            hddn['allsamples'] = ','.join(self.dataset.group.allsamples)
        hddn['primary_samples'] = ','.join(self.primary_sample_names)
        hddn['trait_id'] = self.trait_id
        hddn['trait_display_name'] = self.this_trait.display_name
        hddn['dataset'] = self.dataset.name
        hddn['temp_trait'] = False
        if self.temp_trait:
            hddn['temp_trait'] = True
            hddn['group'] = self.temp_group
            hddn['species'] = self.temp_species
        else:
            hddn['group'] = self.dataset.group.name
            hddn['species'] = self.dataset.group.species
        hddn['use_outliers'] = False
        hddn['method'] = "gemma"
        hddn['mapmethod_rqtl'] = "hk"
        hddn['mapmodel_rqtl'] = "normal"
        hddn['pair_scan'] = ""
        hddn['selected_chr'] = -1
        hddn['mapping_display_all'] = True
        hddn['suggestive'] = 0
        hddn['study_samplelists'] = json.dumps(study_samplelist_json)
        hddn['num_perm'] = 0
        hddn['categorical_vars'] = ""
        if self.categorical_var_list:
            hddn['categorical_vars'] = ",".join(self.categorical_var_list)
        hddn['manhattan_plot'] = ""
        hddn['control_marker'] = ""
        if not self.temp_trait:
            if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
                hddn['control_marker'] = self.nearest_marker
        hddn['do_control'] = False
        hddn['maf'] = 0.05
        hddn['mapping_scale'] = "physic"
        hddn['compare_traits'] = []
        hddn['export_data'] = ""
        hddn['export_format'] = "excel"
        if len(self.scales_in_geno) < 2 and bool(self.scales_in_geno):
            hddn['mapping_scale'] = self.scales_in_geno[list(
                self.scales_in_geno.keys())[0]][0][0]

        # We'll need access to this_trait and hddn in the Jinja2
        # Template, so we put it inside self
        self.hddn = hddn

        js_data = dict(trait_id=self.trait_id,
                       trait_symbol=trait_symbol,
                       max_digits = self.max_digits_by_group,
                       no_decimal_place = self.no_decimal_place,
                       short_description=short_description,
                       unit_type=trait_units,
                       dataset_type=self.dataset.type,
                       species=self.dataset.group.species,
                       scales_in_geno=self.scales_in_geno,
                       data_scale=self.dataset.data_scale,
                       sample_group_types=self.sample_group_types,
                       sample_lists=sample_lists,
                       se_exists=self.sample_groups[0].se_exists,
                       has_num_cases=self.has_num_cases,
                       attributes=self.sample_groups[0].attributes,
                       categorical_attr_exists=self.categorical_attr_exists,
                       categorical_vars=",".join(self.categorical_var_list),
                       num_values=self.num_values,
                       qnorm_values=self.qnorm_vals,
                       zscore_values=self.z_scores,
                       sample_column_width=sample_column_width,
                       temp_uuid=self.temp_uuid)
        self.js_data = js_data

    def get_external_links(self):
        # ZS: There's some weirdness here because some fields don't
        # exist while others are empty strings
        self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if check_if_attr_exists(
            self.this_trait, 'pubmed_id') else None
        self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if check_if_attr_exists(
            self.this_trait, 'geneid') else None
        self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if check_if_attr_exists(
            self.this_trait, 'omim') else None
        self.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if check_if_attr_exists(
            self.this_trait, 'homologeneid') else None

        self.genbank_link = None
        if check_if_attr_exists(self.this_trait, 'genbankid'):
            genbank_id = '|'.join(self.this_trait.genbankid.split('|')[0:10])
            if genbank_id[-1] == '|':
                genbank_id = genbank_id[0:-1]
            self.genbank_link = webqtlConfig.GENBANK_ID % genbank_id

        self.uniprot_link = None
        if check_if_attr_exists(self.this_trait, 'uniprotid'):
            self.uniprot_link = webqtlConfig.UNIPROT_URL % self.this_trait.uniprotid

        self.genotation_link = self.rgd_link = self.phenogen_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None
        self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = self.ensembl_link = None
        if self.this_trait.symbol:
            self.genotation_link = webqtlConfig.GENOTATION_URL % self.this_trait.symbol
            self.gtex_link = webqtlConfig.GTEX_URL % self.this_trait.symbol
            self.string_link = webqtlConfig.STRING_URL % self.this_trait.symbol
            self.panther_link = webqtlConfig.PANTHER_URL % self.this_trait.symbol
            self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol
            self.protein_atlas_link = webqtlConfig.PROTEIN_ATLAS_URL % self.this_trait.symbol

            if self.dataset.group.species == "mouse" or self.dataset.group.species == "human":
                self.rgd_link = webqtlConfig.RGD_URL % (
                    self.this_trait.symbol, self.dataset.group.species.capitalize())
                if self.dataset.group.species == "mouse":
                    self.genemania_link = webqtlConfig.GENEMANIA_URL % (
                        "mus-musculus", self.this_trait.symbol)
                else:
                    self.genemania_link = webqtlConfig.GENEMANIA_URL % (
                        "homo-sapiens", self.this_trait.symbol)

                if self.dataset.group.species == "mouse":
                    self.aba_link = webqtlConfig.ABA_URL % self.this_trait.symbol
                    results = ()
                    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
                        cursor.execute(
                            "SELECT chromosome, txStart, txEnd FROM "
                            "GeneList WHERE geneSymbol = %s",
                            (self.this_trait.symbol,)
                        )
                        results = cursor.fetchone()
                    if results:
                        chr, transcript_start, transcript_end = results
                    else:
                        chr = transcript_start = transcript_end = None

                    if chr and transcript_start and transcript_end and self.this_trait.refseq_transcriptid:
                        transcript_start = int(transcript_start * 1000000)
                        transcript_end = int(transcript_end * 1000000)
                        self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % (
                            'mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end)

            if self.dataset.group.species == "rat":
                self.rgd_link = webqtlConfig.RGD_URL % (
                    self.this_trait.symbol, self.dataset.group.species.capitalize())
                self.phenogen_link = webqtlConfig.PHENOGEN_URL % (
                    self.this_trait.symbol)
                self.genemania_link = webqtlConfig.GENEMANIA_URL % (
                    "rattus-norvegicus", self.this_trait.symbol)

                results = ()
                with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
                    cursor.execute(
                        "SELECT kgID, chromosome, txStart, txEnd "
                        "FROM GeneList_rn33 WHERE geneSymbol = %s",
                        (self.this_trait.symbol,)
                    )
                    if results := cursor.fetchone():
                        kgId, chr, transcript_start, transcript_end = results
                    else:
                        kgId = chr = transcript_start = transcript_end = None

                if chr and transcript_start and transcript_end and kgId:
                    # Convert to bases from megabases
                    transcript_start = int(transcript_start * 1000000)
                    transcript_end = int(transcript_end * 1000000)
                    self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % (
                        'rn7', kgId, chr, transcript_start, transcript_end)

            if self.this_trait.geneid and (self.dataset.group.species == "mouse" or self.dataset.group.species == "rat" or self.dataset.group.species == "human"):
                self.biogps_link = webqtlConfig.BIOGPS_URL % (
                    self.dataset.group.species, self.this_trait.geneid)
                self.gemma_link = webqtlConfig.GEMMA_URL % self.this_trait.geneid

                if self.dataset.group.species == "human":
                    self.aba_link = webqtlConfig.ABA_URL % self.this_trait.geneid

    def build_correlation_tools(self):
        if self.temp_trait == True:
            this_group = self.temp_group
        else:
            this_group = self.dataset.group.name

        # We're checking a string here!
        assert isinstance(this_group, str), "We need a string type thing here"
        if this_group[:3] == 'BXD' and this_group not in webqtlConfig.BXD_GROUP_EXCEPTIONS:
            this_group = 'BXD'

        if this_group:
            if self.temp_trait == True:
                dataset_menu = data_set.datasets(this_group)
            else:
                dataset_menu = data_set.datasets(
                    this_group, self.dataset.group)
            dataset_menu_selected = None
            if len(dataset_menu):
                if self.dataset:
                    dataset_menu_selected = self.dataset.name

            return_results_menu = (100, 200, 500, 1000,
                                   2000, 5000, 10000, 15000, 20000)
            return_results_menu_selected = 500

            self.corr_tools = dict(dataset_menu=dataset_menu,
                                   dataset_menu_selected=dataset_menu_selected,
                                   return_results_menu=return_results_menu,
                                   return_results_menu_selected=return_results_menu_selected,)

    def make_sample_lists(self):

        all_samples_ordered = self.dataset.group.all_samples_ordered()

        parent_f1_samples = []
        if self.dataset.group.parlist and self.dataset.group.f1list:
            parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list

        primary_sample_names = list(all_samples_ordered)

        if not self.temp_trait:
            other_sample_names = []

            for sample in list(self.this_trait.data.keys()):
                if (self.this_trait.data[sample].name2 != self.this_trait.data[sample].name):
                    if ((self.this_trait.data[sample].name2 in primary_sample_names)
                            and (self.this_trait.data[sample].name not in primary_sample_names)):
                        primary_sample_names.append(
                            self.this_trait.data[sample].name)
                        primary_sample_names.remove(
                            self.this_trait.data[sample].name2)

                all_samples_set = set(all_samples_ordered)
                if sample not in all_samples_set:
                    all_samples_ordered.append(sample)
                    other_sample_names.append(sample)

            # CFW is here because the .geno file doesn't properly
            # contain its full list of samples. This should probably
            # be fixed.
            if self.dataset.group.species == "human" or (set(primary_sample_names) == set(parent_f1_samples)) or self.dataset.group.name == "CFW":
                primary_sample_names += other_sample_names
                other_sample_names = []

            if other_sample_names:
                primary_header = "%s Only" % (self.dataset.group.name)
            else:
                primary_header = "Samples"

            primary_samples = SampleList(dataset=self.dataset,
                                         sample_names=primary_sample_names,
                                         this_trait=self.this_trait,
                                         sample_group_type='primary',
                                         header=primary_header)

            # if other_sample_names and self.dataset.group.species !=
            # "human" and self.dataset.group.name != "CFW":
            if len(other_sample_names) > 0:
                other_sample_names.sort()  # Sort other samples
                other_samples = SampleList(dataset=self.dataset,
                                           sample_names=other_sample_names,
                                           this_trait=self.this_trait,
                                           sample_group_type='other',
                                           header="Other")

                self.sample_groups = (primary_samples, other_samples)
            else:
                self.sample_groups = (primary_samples,)
        else:
            primary_samples = SampleList(dataset=self.dataset,
                                         sample_names=primary_sample_names,
                                         this_trait=self.trait_vals,
                                         sample_group_type='primary',
                                         header="%s Only" % (self.dataset.group.name))
            self.sample_groups = (primary_samples,)
        self.primary_sample_names = primary_sample_names
        self.dataset.group.allsamples = all_samples_ordered


def get_trait_vals(sample_list):
    trait_vals = []
    for sample in sample_list:
        try:
            trait_vals.append(float(sample.value))
        except:
            continue

    return trait_vals

def get_max_digits(trait_vals):
    def __max_digits__(these_vals):
        if not bool(these_vals):
            return None
        return len(str(max(these_vals))) - 1

    return [__max_digits__(val) for val in trait_vals], all([val.is_integer() for val in sum(trait_vals, [])])

def normf(trait_vals):
    ranked_vals = ss.rankdata(trait_vals)
    p_list = []
    for i, val in enumerate(trait_vals):
        p_list.append(((i + 1) - 0.5) / len(trait_vals))

    z = ss.norm.ppf(p_list)

    normed_vals = []
    for rank in ranked_vals:
        normed_vals.append("%0.3f" % z[int(rank) - 1])

    return normed_vals

def quantile_normalize_vals(sample_groups, trait_vals):
    qnorm_by_group = []
    for i, sample_type in enumerate(sample_groups):
        qnorm_vals = normf(trait_vals[i])
        qnorm_vals_with_x = []
        counter = 0
        for sample in sample_type.sample_list:
            if sample.display_value == "x":
                qnorm_vals_with_x.append("x")
            else:
                qnorm_vals_with_x.append(qnorm_vals[counter])
                counter += 1

        qnorm_by_group.append(qnorm_vals_with_x)

    return qnorm_by_group


def get_z_scores(sample_groups, trait_vals):
    zscore_by_group = []
    for i, sample_type in enumerate(sample_groups):
        zscores = ss.mstats.zscore(np.array(trait_vals[i])).tolist()
        zscores_with_x = []
        counter = 0
        for sample in sample_type.sample_list:
            if sample.display_value == "x":
                zscores_with_x.append("x")
            else:
                zscores_with_x.append("%0.3f" % zscores[counter])
                counter += 1

        zscore_by_group.append(zscores_with_x)

    return zscore_by_group


def get_nearest_marker(this_trait, this_db):
    this_chr = this_trait.locus_chr
    this_mb = this_trait.locus_mb
    # One option is to take flanking markers, another is to take the
    # two (or one) closest
    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
        cursor.execute(
            "SELECT Geno.Name FROM Geno, GenoXRef, "
            "GenoFreeze WHERE Geno.Chr = %s AND "
            "GenoXRef.GenoId = Geno.Id AND "
            "GenoFreeze.Id = GenoXRef.GenoFreezeId "
            "AND GenoFreeze.Name = %s ORDER BY "
            "ABS( Geno.Mb - %s) LIMIT 1",
            (this_chr, f"{this_db.group.name}Geno", this_mb,)
        )
        if result := cursor.fetchall():
            return result[0][0]
        return ""


def get_table_widths(sample_groups, sample_column_width, has_num_cases=False):
    stats_table_width = 250
    if len(sample_groups) > 1:
        stats_table_width = 450

    trait_table_width = 300 + sample_column_width
    if sample_groups[0].se_exists:
        trait_table_width += 80
    if has_num_cases:
        trait_table_width += 80
    trait_table_width += len(sample_groups[0].attributes) * 88

    return stats_table_width, trait_table_width


def has_num_cases(this_trait):
    has_n = False
    if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno":
        for name, sample in list(this_trait.data.items()):
            if sample.num_cases and sample.num_cases != "1":
                has_n = True
                break

    return has_n


def get_trait_units(this_trait):
    unit_type = ""
    inside_brackets = False
    if this_trait.description_fmt:
        if ("[" in this_trait.description_fmt) and ("]" in this_trait.description_fmt):
            for i in this_trait.description_fmt:
                if inside_brackets:
                    if i != "]":
                        unit_type += i
                    else:
                        inside_brackets = False
                if i == "[":
                    inside_brackets = True

    if unit_type == "":
        unit_type = "value"

    return unit_type


def check_if_attr_exists(the_trait, id_type):
    if hasattr(the_trait, id_type):
        if getattr(the_trait, id_type) == None or getattr(the_trait, id_type) == "":
            return False
        else:
            return True
    else:
        return False


def get_ncbi_summary(this_trait):
    if check_if_attr_exists(this_trait, 'geneid'):
        # ZS: Need to switch this try/except to something that checks
        # the output later
        try:
            response = requests.get(
                "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=%s&retmode=json" % this_trait.geneid)
            summary = json.loads(response.content)[
                'result'][this_trait.geneid]['summary']
            return summary
        except:
            return None
    else:
        return None


def get_categorical_variables(this_trait, sample_list) -> list:
    categorical_var_list = []

    if len(sample_list.attributes) > 0:
        for attribute in sample_list.attributes:
            if len(sample_list.attributes[attribute].distinct_values) < 10:
                categorical_var_list.append(str(sample_list.attributes[attribute].id))

    return categorical_var_list

def get_numerical_variables(this_trait, sample_list) -> list:
    numerical_var_list = []

    if len(sample_list.attributes) > 0:
        for attribute in sample_list.attributes:
            all_numeric = True
            all_none = True
            for attr_val in sample_list.attributes[attribute].distinct_values:
                if not attr_val:
                    continue
                try:
                    val_as_float = float(attr_val)
                    all_none = False
                except:
                    all_numeric = False
                    break
            if all_numeric and not all_none:
                numerical_var_list.append(sample_list.attributes[attribute].name)

    return numerical_var_list

def get_genotype_scales(genofiles):
    geno_scales = {}
    if isinstance(genofiles, list):
        for the_file in genofiles:
            file_location = the_file['location']
            geno_scales[file_location] = get_scales_from_genofile(
                file_location)
    else:
        geno_scales[genofiles] = get_scales_from_genofile(genofiles)

    return geno_scales


def get_scales_from_genofile(file_location):
    geno_path = locate_ignore_error(file_location, 'genotype')
    # ZS: This is just to allow the code to run when
    if not geno_path:
        return [["physic", "Mb"]]
    cm_and_mb_cols_exist = True
    cm_column = None
    mb_column = None
    with open(geno_path, "r") as geno_fh:
        for i, line in enumerate(geno_fh):
            if line[0] == "#" or line[0] == "@":
                # ZS: If the scale is made explicit in the metadata,
                # use that
                if "@scale" in line:
                    scale = line.split(":")[1].strip()
                    if scale == "morgan":
                        return [["morgan", "cM"]]
                    else:
                        return [["physic", "Mb"]]
                else:
                    continue
            if line[:3] == "Chr":
                first_marker_line = i + 1
                if line.split("\t")[2].strip() == "cM":
                    cm_column = 2
                elif line.split("\t")[3].strip() == "cM":
                    cm_column = 3
                if line.split("\t")[2].strip() == "Mb":
                    mb_column = 2
                elif line.split("\t")[3].strip() == "Mb":
                    mb_column = 3
                break

        # ZS: This attempts to check whether the cM and Mb columns are
        # 'real', since some .geno files have one column be a copy of
        # the other column, or have one column that is all 0s
        cm_all_zero = True
        mb_all_zero = True
        cm_mb_all_equal = True
        for i, line in enumerate(geno_fh):
            # ZS: I'm assuming there won't be more than 10 markers
            # where the position is listed as 0
            if first_marker_line <= i < first_marker_line + 10:
                if cm_column:
                    cm_val = line.split("\t")[cm_column].strip()
                    if cm_val != "0":
                        cm_all_zero = False
                if mb_column:
                    mb_val = line.split("\t")[mb_column].strip()
                    if mb_val != "0":
                        mb_all_zero = False
                if cm_column and mb_column:
                    if cm_val != mb_val:
                        cm_mb_all_equal = False
            else:
                if i > first_marker_line + 10:
                    break

    # ZS: This assumes that both won't be all zero, since if that's
    # the case mapping shouldn't be an option to begin with
    if mb_all_zero:
        return [["morgan", "cM"]]
    elif cm_mb_all_equal:
        return [["physic", "Mb"]]
    elif cm_and_mb_cols_exist:
        return [["physic", "Mb"], ["morgan", "cM"]]
    else:
        return [["physic", "Mb"]]



def get_diff_of_vals(new_vals: Dict, trait_id: str) -> Dict:
    """ Get the diff between current sample values and the values in the DB

    Given a dict of the changed values and the trait/dataset ID, return a Dict
    with keys corresponding to each sample with a changed value and a value
    that is a dict with keys for the old_value and new_value

    """

    trait_name = trait_id.split(":")[0]
    dataset_name = trait_id.split(":")[1]
    trait_ob = create_trait(name=trait_name, dataset_name=dataset_name)

    old_vals = {sample : trait_ob.data[sample].value for sample in trait_ob.data}

    shared_samples = set.union(set(new_vals.keys()), set(old_vals.keys()))

    diff_dict = {}
    for sample in shared_samples:
        try:
            new_val = round(float(new_vals[sample]), 3)
        except:
            new_val = "x"
        try:
            old_val = round(float(old_vals[sample]), 3)
        except:
            old_val = "x"

        if new_val != old_val:
            diff_dict[sample] = {
                "new_val": new_val,
                "old_val": old_val
            }

    return diff_dict