delete unwanted correlation stuff (#5)

* delete unwanted correlation stuff

* Refactor/clean up correlations (#4)

* initial commit for Refactor/clean-up-correlation

* add python scipy dependency

* initial commit for sample correlation

* initial commit for sample correlation endpoint

* initial commit for integration and unittest

* initial commit for registering  correlation blueprint

* add and modify unittest and integration tests for correlation

* Add compute compute_all_sample_corr   method for correlation

* add scipy to requirement txt file

* add tissue correlation for trait list

* add unittest for tissue correlation

* add lit correlation for trait list

* add unittests for lit correlation for trait list

* modify lit correlarion for trait list

* add unittests for lit correlation for trait list

* add correlation metho  in dynamic url

* add file format for expected structure input  while doing sample correlation

* modify input data structure -> add  trait id

* update tests for sample r correlation

* add compute all lit correlation method

* add endpoint for computing lit_corr

* add unit and integration tests for computing lit corr

* add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation

* add unittest and integration tests for tissue correlation

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>

* update guix scm file

* fix pylint error for correlations api

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>

6 files changed, 0 insertions, 1490 deletions

diff --git a/gn3/base/__init__.py b/gn3/base/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/gn3/base/__init__.py
+++ /dev/null
diff --git a/gn3/base/data_set.py b/gn3/base/data_set.py
deleted file mode 100644
index 01913f2..0000000
--- a/gn3/base/data_set.py
+++ /dev/null
@@ -1,882 +0,0 @@
-
-import json
-import math
-import collections
-import requests
-from redis import Redis
-from flask import g
-from gn3.utility.db_tools import escape
-from gn3.utility.db_tools import mescape
-from gn3.utility.db_tools import create_in_clause
-from gn3.utility.tools import locate_ignore_error
-from gn3.db.calls import fetch1
-from gn3.db.calls import fetchone
-from gn3.db.webqtlDatabaseFunction import retrieve_species
-from gn3.utility import chunks
-
-from gn3.utility import get_group_samplelists
-from gn3.base.species import TheSpecies
-r = Redis()
-
-# should probably move this to its own configuration files
-
-USE_REDIS = True
-
-# todo move to config file
-GN2_BASE_URL = "https://genenetwork.org/"
-
-DS_NAME_MAP = {}
-
-# pylint: disable-all
-#todo file not linted
-# pylint: disable=C0103 
-
-
-
-def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None):
-
-    if dataset_name == "Temp":
-        dataset_type = "Temp"
-
-    if dataset_type is None:
-        dataset_type = Dataset_Getter(dataset_name)
-    dataset_ob = DS_NAME_MAP[dataset_type]
-    dataset_class = globals()[dataset_ob]
-
-    if dataset_type == "Temp":
-        results = dataset_class(dataset_name, get_samplelist, group_name)
-
-    else:
-        results = dataset_class(dataset_name, get_samplelist)
-
-    return results
-
-
-class DatasetType:
-    def __init__(self, redis_instance):
-        self.redis_instance = redis_instance
-        self.datasets = {}
-
-        data = self.redis_instance.get("dataset_structure")
-        if data:
-            self.datasets = json.loads(data)
-
-        else:
-
-            try:
-
-                data = json.loads(requests.get(
-                    GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content)
-
-                # todo:Refactor code below n^4 loop
-
-                for species in data["datasets"]:
-                    for group in data["datasets"][species]:
-                        for dataset_type in data['datasets'][species][group]:
-                            for dataset in data['datasets'][species][group][dataset_type]:
-
-                                short_dataset_name = dataset[1]
-                                if dataset_type == "Phenotypes":
-                                    new_type = "Publish"
-
-                                elif dataset_type == "Genotypes":
-                                    new_type = "Geno"
-                                else:
-                                    new_type = "ProbeSet"
-
-                                self.datasets[short_dataset_name] = new_type
-
-            except Exception as e:
-                raise e
-
-            self.redis_instance.set(
-                "dataset_structure", json.dumps(self.datasets))
-
-    def set_dataset_key(self, t, name):
-        """If name is not in the object's dataset dictionary, set it, and update
-    dataset_structure in Redis
-
-    args:
-      t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
-         'other_pheno', 'geno'
-      name: The name of the key to inserted in the datasets dictionary
-
-    """
-
-        sql_query_mapping = {
-            'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ +
-                          """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """),
-            'pheno': ("""SELECT InfoFiles.GN_AccesionId """ +
-                      """FROM InfoFiles, PublishFreeze, InbredSet """ +
-                      """WHERE InbredSet.Name = '{}' AND """ +
-                      """PublishFreeze.InbredSetId = InbredSet.Id AND """ +
-                      """InfoFiles.InfoPageName = PublishFreeze.Name"""),
-            'other_pheno': ("""SELECT PublishFreeze.Name """ +
-                            """FROM PublishFreeze, InbredSet """ +
-                            """WHERE InbredSet.Name = '{}' AND """ +
-                            """PublishFreeze.InbredSetId = InbredSet.Id"""),
-            'geno':  ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ +
-                      """GenoFreeze.Name = "{}" """)
-        }
-
-        dataset_name_mapping = {
-            "mrna_expr": "ProbeSet",
-            "pheno": "Publish",
-            "other_pheno": "Publish",
-            "geno": "Geno",
-        }
-
-        group_name = name
-        if t in ['pheno', 'other_pheno']:
-            group_name = name.replace("Publish", "")
-
-        results = g.db.execute(
-            sql_query_mapping[t].format(group_name)).fetchone()
-        if results:
-            self.datasets[name] = dataset_name_mapping[t]
-            self.redis_instance.set(
-                "dataset_structure", json.dumps(self.datasets))
-
-            return True
-
-        return None
-
-    def __call__(self, name):
-        if name not in self.datasets:
-            for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
-
-                if(self.set_dataset_key(t, name)):
-                    # This has side-effects, with the end result being a truth-y value
-                    break
-
-        return self.datasets.get(name, None)
-
-
-# Do the intensive work at  startup one time only
-# could replace the code below
-Dataset_Getter = DatasetType(r)
-
-
-class DatasetGroup:
-    """
-    Each group has multiple datasets; each species has multiple groups.
-
-    For example, Mouse has multiple groups (BXD, BXA, etc), and each group
-    has multiple datasets associated with it.
-
-    """
-
-    def __init__(self, dataset, name=None):
-        """This sets self.group and self.group_id"""
-        if name == None:
-            self.name, self.id, self.genetic_type = fetchone(
-                dataset.query_for_group)
-
-        else:
-            self.name, self.id, self.genetic_type = fetchone(
-                "SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
-
-        if self.name == 'BXD300':
-            self.name = "BXD"
-
-        self.f1list = None
-
-        self.parlist = None
-
-        self.get_f1_parent_strains()
-
-        # remove below not used in correlation
-
-        self.mapping_id, self.mapping_names = self.get_mapping_methods()
-
-        self.species = retrieve_species(self.name)
-
-    def get_f1_parent_strains(self):
-        try:
-            # should import ParInfo
-            raise e
-            # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
-            f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
-        except Exception as e:
-            f1 = f12 = maternal = paternal = None
-
-        if f1 and f12:
-            self.f1list = [f1, f12]
-
-        if maternal and paternal:
-            self.parlist = [maternal, paternal]
-
-    def get_mapping_methods(self):
-        mapping_id = g.db.execute(
-            "select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
-
-        if mapping_id == "1":
-            mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
-        elif mapping_id == "2":
-            mapping_names = ["GEMMA"]
-
-        elif mapping_id == "3":
-            mapping_names = ["R/qtl"]
-
-        elif mapping_id == "4":
-            mapping_names = ["GEMMA", "PLINK"]
-
-        else:
-            mapping_names = []
-
-        return mapping_id, mapping_names
-
-    def get_samplelist(self):
-        result = None
-        key = "samplelist:v3:" + self.name
-        if USE_REDIS:
-            result = r.get(key)
-
-        if result is not None:
-
-            self.samplelist = json.loads(result)
-
-        else:
-            # logger.debug("Cache not hit")
-            # should enable logger
-            genotype_fn = locate_ignore_error(self.name+".geno", 'genotype')
-            if genotype_fn:
-                self.samplelist = get_group_samplelists.get_samplelist(
-                    "geno", genotype_fn)
-
-            else:
-                self.samplelist = None
-
-            if USE_REDIS:
-                r.set(key, json.dumps(self.samplelist))
-                r.expire(key, 60*5)
-
-
-class DataSet:
-    """
-    DataSet class defines a dataset in webqtl, can be either Microarray,
-    Published phenotype, genotype, or user input dataset(temp)
-
-    """
-
-    def __init__(self, name, get_samplelist=True, group_name=None):
-
-        assert name, "Need a name"
-        self.name = name
-        self.id = None
-        self.shortname = None
-        self.fullname = None
-        self.type = None
-        self.data_scale = None  # ZS: For example log2
-
-        self.setup()
-
-        if self.type == "Temp":  # Need to supply group name as input if temp trait
-            # sets self.group and self.group_id and gets genotype
-            self.group = DatasetGroup(self, name=group_name)
-        else:
-            self.check_confidentiality()
-            self.retrieve_other_names()
-            # sets self.group and self.group_id and gets genotype
-            self.group = DatasetGroup(self)
-            self.accession_id = self.get_accession_id()
-        if get_samplelist == True:
-            self.group.get_samplelist()
-        self.species = TheSpecies(self)
-
-    def get_desc(self):
-        """Gets overridden later, at least for Temp...used by trait's get_given_name"""
-        return None
-
-
-    def get_accession_id(self):
-        if self.type == "Publish":
-            results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
-                        InbredSet.Name = %s and
-                        PublishFreeze.InbredSetId = InbredSet.Id and
-                        InfoFiles.InfoPageName = PublishFreeze.Name and
-                        PublishFreeze.public > 0 and
-                        PublishFreeze.confidentiality < 1 order by
-                        PublishFreeze.CreateTime desc""", (self.group.name)).fetchone()
-        elif self.type == "Geno":
-            results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
-                        InbredSet.Name = %s and
-                        GenoFreeze.InbredSetId = InbredSet.Id and
-                        InfoFiles.InfoPageName = GenoFreeze.ShortName and
-                        GenoFreeze.public > 0 and
-                        GenoFreeze.confidentiality < 1 order by
-                        GenoFreeze.CreateTime desc""", (self.group.name)).fetchone()
-        else:
-            results = None
-
-        if results != None:
-            return str(results[0])
-        else:
-            return "None"
-
-    def retrieve_other_names(self):
-        """This method fetches the the dataset names in search_result.
-
-        If the data set name parameter is not found in the 'Name' field of
-        the data set table, check if it is actually the FullName or
-        ShortName instead.
-
-        This is not meant to retrieve the data set info if no name at
-        all is passed.
-
-        """
-
-        try:
-            if self.type == "ProbeSet":
-                query_args = tuple(escape(x) for x in (
-                    self.name,
-                    self.name,
-                    self.name))
-
-                self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
-    SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
-    FROM ProbeSetFreeze, ProbeFreeze, Tissue
-    WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
-    AND ProbeFreeze.TissueId = Tissue.Id
-    AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
-                """ % (query_args), "/dataset/"+self.name+".json",
-                    lambda r: (r["id"], r["name"], r["full_name"],
-                               r["short_name"], r["data_scale"], r["tissue"])
-                )
-            else:
-                query_args = tuple(escape(x) for x in (
-                    (self.type + "Freeze"),
-                    self.name,
-                    self.name,
-                    self.name))
-
-                self.tissue = "N/A"
-                self.id, self.name, self.fullname, self.shortname = fetchone("""
-                        SELECT Id, Name, FullName, ShortName
-                        FROM %s
-                        WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
-                    """ % (query_args))
-
-        except TypeError as e:
-            logger.debug(
-                "Dataset {} is not yet available in GeneNetwork.".format(self.name))
-            pass
-
-    def get_trait_data(self, sample_list=None):
-        if sample_list:
-            self.samplelist = sample_list
-        else:
-            self.samplelist = self.group.samplelist
-
-        if self.group.parlist != None and self.group.f1list != None:
-            if (self.group.parlist + self.group.f1list) in self.samplelist:
-                self.samplelist += self.group.parlist + self.group.f1list
-
-        query = """
-            SELECT Strain.Name, Strain.Id FROM Strain, Species
-            WHERE Strain.Name IN {}
-            and Strain.SpeciesId=Species.Id
-            and Species.name = '{}'
-            """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
-        # logger.sql(query)
-        results = dict(g.db.execute(query).fetchall())
-        sample_ids = [results[item] for item in self.samplelist]
-
-        # MySQL limits the number of tables that can be used in a join to 61,
-        # so we break the sample ids into smaller chunks
-        # Postgres doesn't have that limit, so we can get rid of this after we transition
-        chunk_size = 50
-        number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
-        trait_sample_data = []
-        for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
-            if self.type == "Publish":
-                dataset_type = "Phenotype"
-            else:
-                dataset_type = self.type
-            temp = ['T%s.value' % item for item in sample_ids_step]
-            if self.type == "Publish":
-                query = "SELECT {}XRef.Id,".format(escape(self.type))
-            else:
-                query = "SELECT {}.Name,".format(escape(dataset_type))
-            data_start_pos = 1
-            query += ', '.join(temp)
-            query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
-                                                                     self.type,
-                                                                     self.type))
-
-            for item in sample_ids_step:
-                query += """
-                        left join {}Data as T{} on T{}.Id = {}XRef.DataId
-                        and T{}.StrainId={}\n
-                        """.format(*mescape(self.type, item, item, self.type, item, item))
-
-            if self.type == "Publish":
-                query += """
-                        WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId
-                        and {}Freeze.Name = '{}'
-                        and {}.Id = {}XRef.{}Id
-                        order by {}.Id
-                        """.format(*mescape(self.type, self.type, self.type, self.name,
-                                            dataset_type, self.type, dataset_type, dataset_type))
-            else:
-                query += """
-                        WHERE {}XRef.{}FreezeId = {}Freeze.Id
-                        and {}Freeze.Name = '{}'
-                        and {}.Id = {}XRef.{}Id
-                        order by {}.Id
-                        """.format(*mescape(self.type, self.type, self.type, self.type,
-                                            self.name, dataset_type, self.type, self.type, dataset_type))
-
-            results = g.db.execute(query).fetchall()
-            trait_sample_data.append(results)
-
-        trait_count = len(trait_sample_data[0])
-        self.trait_data = collections.defaultdict(list)
-
-        # put all of the separate data together into a dictionary where the keys are
-        # trait names and values are lists of sample values
-        for trait_counter in range(trait_count):
-            trait_name = trait_sample_data[0][trait_counter][0]
-            for chunk_counter in range(int(number_chunks)):
-                self.trait_data[trait_name] += (
-                    trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
-
-
-class MrnaAssayDataSet(DataSet):
-    '''
-    An mRNA Assay is a quantitative assessment (assay) associated with an mRNA trait
-
-    This used to be called ProbeSet, but that term only refers specifically to the Affymetrix
-    platform and is far too specific.
-
-    '''
-    DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet'
-
-    def setup(self):
-        # Fields in the database table
-        self.search_fields = ['Name',
-                              'Description',
-                              'Probe_Target_Description',
-                              'Symbol',
-                              'Alias',
-                              'GenbankId',
-                              'UniGeneId',
-                              'RefSeq_TranscriptId']
-
-        # Find out what display_fields is
-        self.display_fields = ['name', 'symbol',
-                               'description', 'probe_target_description',
-                               'chr', 'mb',
-                               'alias', 'geneid',
-                               'genbankid', 'unigeneid',
-                               'omim', 'refseq_transcriptid',
-                               'blatseq', 'targetseq',
-                               'chipid', 'comments',
-                               'strand_probe', 'strand_gene',
-                               'proteinid', 'uniprotid',
-                               'probe_set_target_region',
-                               'probe_set_specificity',
-                               'probe_set_blat_score',
-                               'probe_set_blat_mb_start',
-                               'probe_set_blat_mb_end',
-                               'probe_set_strand',
-                               'probe_set_note_by_rw',
-                               'flag']
-
-        # Fields displayed in the search results table header
-        self.header_fields = ['Index',
-                              'Record',
-                              'Symbol',
-                              'Description',
-                              'Location',
-                              'Mean',
-                              'Max LRS',
-                              'Max LRS Location',
-                              'Additive Effect']
-
-        # Todo: Obsolete or rename this field
-        self.type = 'ProbeSet'
-
-        self.query_for_group = '''
-                        SELECT
-                                InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
-                        FROM
-                                InbredSet, ProbeSetFreeze, ProbeFreeze
-                        WHERE
-                                ProbeFreeze.InbredSetId = InbredSet.Id AND
-                                ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
-                                ProbeSetFreeze.Name = "%s"
-                ''' % escape(self.name)
-
-    def check_confidentiality(self):
-        return geno_mrna_confidentiality(self)
-
-    def get_trait_info(self, trait_list=None, species=''):
-
-        #  Note: setting trait_list to [] is probably not a great idea.
-        if not trait_list:
-            trait_list = []
-
-        for this_trait in trait_list:
-
-            if not this_trait.haveinfo:
-                this_trait.retrieveInfo(QTL=1)
-
-            if not this_trait.symbol:
-                this_trait.symbol = "N/A"
-
-            # XZ, 12/08/2008: description
-            # XZ, 06/05/2009: Rob asked to add probe target description
-            description_string = str(
-                str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
-            target_string = str(
-                str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
-
-            if len(description_string) > 1 and description_string != 'None':
-                description_display = description_string
-            else:
-                description_display = this_trait.symbol
-
-            if (len(description_display) > 1 and description_display != 'N/A' and
-                    len(target_string) > 1 and target_string != 'None'):
-                description_display = description_display + '; ' + target_string.strip()
-
-            # Save it for the jinja2 template
-            this_trait.description_display = description_display
-
-            if this_trait.chr and this_trait.mb:
-                this_trait.location_repr = 'Chr%s: %.6f' % (
-                    this_trait.chr, float(this_trait.mb))
-
-            # Get mean expression value
-            query = (
-                """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
-                where ProbeSetXRef.ProbeSetFreezeId = %s and
-                ProbeSet.Id = ProbeSetXRef.ProbeSetId and
-                ProbeSet.Name = '%s'
-            """ % (escape(str(this_trait.dataset.id)),
-                   escape(this_trait.name)))
-
-            #logger.debug("query is:", pf(query))
-            logger.sql(query)
-            result = g.db.execute(query).fetchone()
-
-            mean = result[0] if result else 0
-
-            if mean:
-                this_trait.mean = "%2.3f" % mean
-
-            # LRS and its location
-            this_trait.LRS_score_repr = 'N/A'
-            this_trait.LRS_location_repr = 'N/A'
-
-            # Max LRS and its Locus location
-            if this_trait.lrs and this_trait.locus:
-                query = """
-                    select Geno.Chr, Geno.Mb from Geno, Species
-                    where Species.Name = '{}' and
-                        Geno.Name = '{}' and
-                        Geno.SpeciesId = Species.Id
-                """.format(species, this_trait.locus)
-                logger.sql(query)
-                result = g.db.execute(query).fetchone()
-
-                if result:
-                    lrs_chr, lrs_mb = result
-                    this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
-                    this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
-                        lrs_chr, float(lrs_mb))
-
-        return trait_list
-
-    def retrieve_sample_data(self, trait):
-        query = """
-                    SELECT
-                            Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
-                    FROM
-                            (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
-                    left join ProbeSetSE on
-                            (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
-                    left join NStrain on
-                            (NStrain.DataId = ProbeSetData.Id AND
-                            NStrain.StrainId = ProbeSetData.StrainId)
-                    WHERE
-                            ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                            ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-                            ProbeSetFreeze.Name = '%s' AND
-                            ProbeSetXRef.DataId = ProbeSetData.Id AND
-                            ProbeSetData.StrainId = Strain.Id
-                    Order BY
-                            Strain.Name
-                    """ % (escape(trait), escape(self.name))
-        # logger.sql(query)
-        results = g.db.execute(query).fetchall()
-        #logger.debug("RETRIEVED RESULTS HERE:", results)
-        return results
-
-    def retrieve_genes(self, column_name):
-        query = """
-                    select ProbeSet.Name, ProbeSet.%s
-                    from ProbeSet,ProbeSetXRef
-                    where ProbeSetXRef.ProbeSetFreezeId = %s and
-                    ProbeSetXRef.ProbeSetId=ProbeSet.Id;
-                """ % (column_name, escape(str(self.id)))
-        # logger.sql(query)
-        results = g.db.execute(query).fetchall()
-
-        return dict(results)
-
-
-class TempDataSet(DataSet):
-    '''Temporary user-generated data set'''
-
-    DS_NAME_MAP['Temp'] = 'TempDataSet'
-
-    def setup(self):
-        self.search_fields = ['name',
-                              'description']
-
-        self.display_fields = ['name',
-                               'description']
-
-        self.header_fields = ['Name',
-                              'Description']
-
-        self.type = 'Temp'
-
-        # Need to double check later how these are used
-        self.id = 1
-        self.fullname = 'Temporary Storage'
-        self.shortname = 'Temp'
-
-
-class PhenotypeDataSet(DataSet):
-    DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
-
-    def setup(self):
-
-        #logger.debug("IS A PHENOTYPEDATASET")
-
-        # Fields in the database table
-        self.search_fields = ['Phenotype.Post_publication_description',
-                              'Phenotype.Pre_publication_description',
-                              'Phenotype.Pre_publication_abbreviation',
-                              'Phenotype.Post_publication_abbreviation',
-                              'PublishXRef.mean',
-                              'Phenotype.Lab_code',
-                              'Publication.PubMed_ID',
-                              'Publication.Abstract',
-                              'Publication.Title',
-                              'Publication.Authors',
-                              'PublishXRef.Id']
-
-        # Figure out what display_fields is
-        self.display_fields = ['name', 'group_code',
-                               'pubmed_id',
-                               'pre_publication_description',
-                               'post_publication_description',
-                               'original_description',
-                               'pre_publication_abbreviation',
-                               'post_publication_abbreviation',
-                               'mean',
-                               'lab_code',
-                               'submitter', 'owner',
-                               'authorized_users',
-                               'authors', 'title',
-                               'abstract', 'journal',
-                               'volume', 'pages',
-                               'month', 'year',
-                               'sequence', 'units', 'comments']
-
-        # Fields displayed in the search results table header
-        self.header_fields = ['Index',
-                              'Record',
-                              'Description',
-                              'Authors',
-                              'Year',
-                              'Max LRS',
-                              'Max LRS Location',
-                              'Additive Effect']
-
-        self.type = 'Publish'
-
-        self.query_for_group = '''
-                            SELECT
-                                    InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
-                            FROM
-                                    InbredSet, PublishFreeze
-                            WHERE
-                                    PublishFreeze.InbredSetId = InbredSet.Id AND
-                                    PublishFreeze.Name = "%s"
-                    ''' % escape(self.name)
-
-    def check_confidentiality(self):
-        # (Urgently?) Need to write this
-        pass
-
-    def get_trait_info(self, trait_list, species=''):
-        for this_trait in trait_list:
-
-            if not this_trait.haveinfo:
-                this_trait.retrieve_info(get_qtl_info=True)
-
-            description = this_trait.post_publication_description
-
-            # If the dataset is confidential and the user has access to confidential
-            # phenotype traits, then display the pre-publication description instead
-            # of the post-publication description
-            if this_trait.confidential:
-                this_trait.description_display = ""
-                continue   # todo for now, because no authorization features
-
-                if not webqtlUtil.has_access_to_confidentail_phenotype_trait(
-                        privilege=self.privilege,
-                        userName=self.userName,
-                        authorized_users=this_trait.authorized_users):
-
-                    description = this_trait.pre_publication_description
-
-            if len(description) > 0:
-                this_trait.description_display = description.strip()
-            else:
-                this_trait.description_display = ""
-
-            if not this_trait.year.isdigit():
-                this_trait.pubmed_text = "N/A"
-            else:
-                this_trait.pubmed_text = this_trait.year
-
-            if this_trait.pubmed_id:
-                this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
-
-            # LRS and its location
-            this_trait.LRS_score_repr = "N/A"
-            this_trait.LRS_location_repr = "N/A"
-
-            if this_trait.lrs:
-                query = """
-                    select Geno.Chr, Geno.Mb from Geno, Species
-                    where Species.Name = '%s' and
-                        Geno.Name = '%s' and
-                        Geno.SpeciesId = Species.Id
-                """ % (species, this_trait.locus)
-
-                result = g.db.execute(query).fetchone()
-
-                if result:
-                    if result[0] and result[1]:
-                        LRS_Chr = result[0]
-                        LRS_Mb = result[1]
-
-                        this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
-                        this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
-                            LRS_Chr, float(LRS_Mb))
-
-    def retrieve_sample_data(self, trait):
-        query = """
-                    SELECT
-                            Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
-                    FROM
-                            (PublishData, Strain, PublishXRef, PublishFreeze)
-                    left join PublishSE on
-                            (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
-                    left join NStrain on
-                            (NStrain.DataId = PublishData.Id AND
-                            NStrain.StrainId = PublishData.StrainId)
-                    WHERE
-                            PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-                            PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
-                            PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id
-                    Order BY
-                            Strain.Name
-                    """
-
-        results = g.db.execute(query, (trait, self.id)).fetchall()
-        return results
-
-
-class GenotypeDataSet(DataSet):
-    DS_NAME_MAP['Geno'] = 'GenotypeDataSet'
-
-    def setup(self):
-        # Fields in the database table
-        self.search_fields = ['Name',
-                              'Chr']
-
-        # Find out what display_fields is
-        self.display_fields = ['name',
-                               'chr',
-                               'mb',
-                               'source2',
-                               'sequence']
-
-        # Fields displayed in the search results table header
-        self.header_fields = ['Index',
-                              'ID',
-                              'Location']
-
-        # Todo: Obsolete or rename this field
-        self.type = 'Geno'
-
-        self.query_for_group = '''
-                SELECT
-                        InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
-                FROM
-                        InbredSet, GenoFreeze
-                WHERE
-                        GenoFreeze.InbredSetId = InbredSet.Id AND
-                        GenoFreeze.Name = "%s"
-                ''' % escape(self.name)
-
-    def check_confidentiality(self):
-        return geno_mrna_confidentiality(self)
-
-    def get_trait_info(self, trait_list, species=None):
-        for this_trait in trait_list:
-            if not this_trait.haveinfo:
-                this_trait.retrieveInfo()
-
-            if this_trait.chr and this_trait.mb:
-                this_trait.location_repr = 'Chr%s: %.6f' % (
-                    this_trait.chr, float(this_trait.mb))
-
-    def retrieve_sample_data(self, trait):
-        query = """
-                    SELECT
-                            Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
-                    FROM
-                            (GenoData, GenoFreeze, Strain, Geno, GenoXRef)
-                    left join GenoSE on
-                            (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
-                    WHERE
-                            Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND
-                            GenoXRef.GenoFreezeId = GenoFreeze.Id AND
-                            GenoFreeze.Name = %s AND
-                            GenoXRef.DataId = GenoData.Id AND
-                            GenoData.StrainId = Strain.Id
-                    Order BY
-                            Strain.Name
-                    """
-        results = g.db.execute(query,
-                               (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
-                                trait, self.name)).fetchall()
-        return results
-
-
-def geno_mrna_confidentiality(ob):
-    dataset_table = ob.type + "Freeze"
-    #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
-
-    query = '''SELECT Id, Name, FullName, confidentiality,
-                        AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
-    #
-    result = g.db.execute(query)
-
-    (_dataset_id,
-     _name,
-     _full_name,
-     confidential,
-     _authorized_users) = result.fetchall()[0]
-
-    if confidential:
-        return True
diff --git a/gn3/base/mrna_assay_tissue_data.py b/gn3/base/mrna_assay_tissue_data.py
deleted file mode 100644
index 0f51ade..0000000
--- a/gn3/base/mrna_assay_tissue_data.py
+++ /dev/null
@@ -1,94 +0,0 @@
-
-# pylint: disable-all
-import collections
-
-from flask import g
-
-from gn3.utility.db_tools import create_in_clause
-from gn3.utility.db_tools import escape
-from gn3.utility.bunch import Bunch
-
-
-# from utility.logger import getLogger
-# logger = getLogger(__name__ )
-
-class MrnaAssayTissueData(object):
-
-    def __init__(self, gene_symbols=None):
-        self.gene_symbols = gene_symbols
-        if self.gene_symbols == None:
-            self.gene_symbols = []
-
-        self.data = collections.defaultdict(Bunch)
-
-        query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
-                        from (
-                        select Symbol, max(Mean) as maxmean
-                        from TissueProbeSetXRef
-                        where TissueProbeSetFreezeId=1 and '''
-
-        # Note that inner join is necessary in this query to get distinct record in one symbol group
-        # with highest mean value
-        # Due to the limit size of TissueProbeSetFreezeId table in DB,
-        # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
-        if len(gene_symbols) == 0:
-            query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
-                as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
-                and t.Mean = x.maxmean;
-                    '''
-        else:
-            in_clause = create_in_clause(gene_symbols)
-
-            # ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
-            query += ''' Symbol in {} group by Symbol)
-                as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
-                and t.Mean = x.maxmean;
-                    '''.format(in_clause)
-
-        results = g.db.execute(query).fetchall()
-
-        lower_symbols = []
-        for gene_symbol in gene_symbols:
-            if gene_symbol != None:
-                lower_symbols.append(gene_symbol.lower())
-
-        for result in results:
-            symbol = result[0]
-            if symbol.lower() in lower_symbols:
-                symbol = symbol.lower()
-
-                self.data[symbol].gene_id = result.GeneId
-                self.data[symbol].data_id = result.DataId
-                self.data[symbol].chr = result.Chr
-                self.data[symbol].mb = result.Mb
-                self.data[symbol].description = result.description
-                self.data[symbol].probe_target_description = result.Probe_Target_Description
-
-    ###########################################################################
-    # Input: cursor, symbolList (list), dataIdDict(Dict)
-    # output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
-    #        key is symbol, value is one list of expression values of one probeSet;
-    # function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
-    # Attention! All keys are lower case!
-    ###########################################################################
-
-    def get_symbol_values_pairs(self):
-        id_list = [self.data[symbol].data_id for symbol in self.data]
-
-        symbol_values_dict = {}
-
-        if len(id_list) > 0:
-            query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
-                       FROM TissueProbeSetXRef, TissueProbeSetData
-                       WHERE TissueProbeSetData.Id IN {} and
-                             TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(create_in_clause(id_list))
-
-            results = g.db.execute(query).fetchall()
-            for result in results:
-                if result.Symbol.lower() not in symbol_values_dict:
-                    symbol_values_dict[result.Symbol.lower()] = [result.value]
-                else:
-                    symbol_values_dict[result.Symbol.lower()].append(
-                        result.value)
-
-        return symbol_values_dict
diff --git a/gn3/base/species.py b/gn3/base/species.py
deleted file mode 100644
index 9fb08fb..0000000
--- a/gn3/base/species.py
+++ /dev/null
@@ -1,64 +0,0 @@
-
-# pylint: disable-all
-import collections
-from flask import g
-from dataclasses import dataclass
-
-class TheSpecies:
-    def __init__(self, dataset=None, species_name=None):
-        if species_name is not None:
-            self.name = species_name
-
-            self.chromosomes = Chromosomes(species=self.name)
-
-        else:
-            self.dataset = dataset
-            self.chromosomes = Chromosomes(dataset=self.dataset)
-
-
-class Chromosomes:
-    def __init__(self, dataset=None, species=None):
-        self.chromosomes = collections.OrderedDict()
-
-        if species is not None:
-            query = """
-                Select
-                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species
-                where
-                        Chr_Length.SpeciesId = Species.SpeciesId AND
-                        Species.Name = '%s'
-                Order by OrderId
-                """ % species.capitalize()
-
-        else:
-            self.dataset = dataset
-
-            query = """
-                Select
-                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
-                where
-                        Chr_Length.SpeciesId = InbredSet.SpeciesId AND
-                        InbredSet.Name = '%s'
-                Order by OrderId
-                """ % self.dataset.group.name
-
-            # logger.sql(query)
-
-            results = g.db.execute(query).fetchall()
-
-            for item in results:
-                self.chromosomes[item.OrderId] = IndChromosome(
-                    item.Name, item.Length)
-
-
-# @dataclass
-class IndChromosome:
-    def __init__(self,name,length):
-        self.name= name
-        self.length = length
-
-    @property
-    def mb_length(self):
-        """Chromosome length in megabases"""
-        return self.length/ 1000000
-    
diff --git a/gn3/base/trait.py b/gn3/base/trait.py
deleted file mode 100644
index f4be61c..0000000
--- a/gn3/base/trait.py
+++ /dev/null
@@ -1,366 +0,0 @@
-
-# pylint: disable-all
-from flask import g
-from redis import Redis
-from gn3.utility.db_tools import escape
-from gn3.base.webqtlCaseData import webqtlCaseData
-
-
-def check_resource_availability(dataset, name=None):
-
-    # todo add code for this
-    # should probably work on this has to do with authentication
-    return {'data': ['no-access', 'view'], 'metadata': ['no-access', 'view'], 'admin': ['not-admin']}
-
-
-def create_trait(**kw):
-    # work on check resource availability deals with authentication
-    assert bool(kw.get("dataset")) != bool(
-        kw.get('dataset_name')), "Needs dataset ob. or name"
-
-    assert bool(kw.get("name")), "Need trait name"
-
-    if kw.get('dataset_name'):
-        if kw.get('dataset_name') != "Temp":
-            dataset = create_dataset(kw.get('dataset_name'))
-    else:
-        dataset = kw.get('dataset')
-
-    if dataset.type == 'Publish':
-        permissions = check_resource_availability(
-            dataset, kw.get('name'))
-    else:
-        permissions = check_resource_availability(dataset)
-
-    if "view" in permissions['data']:
-        the_trait = GeneralTrait(**kw)
-        if the_trait.dataset.type != "Temp":
-            the_trait = retrieve_trait_info(
-                the_trait,
-                the_trait.dataset,
-                get_qtl_info=kw.get('get_qtl_info'))
-
-
-            return the_trait
-
-    return None
-
-
-class GeneralTrait:
-    def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
-        assert bool(kw.get('dataset')) != bool(
-            kw.get('dataset_name')), "Needs dataset ob. or name"
-        # Trait ID, ProbeSet ID, Published ID, etc.
-        self.name = kw.get('name')
-        if kw.get('dataset_name'):
-            if kw.get('dataset_name') == "Temp":
-                temp_group = self.name.split("_")[2]
-                self.dataset = create_dataset(
-                    dataset_name="Temp",
-                    dataset_type="Temp",
-                    group_name=temp_group)
-
-            else:
-                self.dataset = create_dataset(kw.get('dataset_name'))
-
-        else:
-            self.dataset = kw.get("dataset")
-
-        self.cellid = kw.get('cellid')
-        self.identification = kw.get('identification', 'un-named trait')
-        self.haveinfo = kw.get('haveinfo', False)
-        self.sequence = kw.get('sequence')
-        self.data = kw.get('data', {})
-        self.view = True
-
-        # Sets defaults
-        self.locus = None
-        self.lrs = None
-        self.pvalue = None
-        self.mean = None
-        self.additive = None
-        self.num_overlap = None
-        self.strand_probe = None
-        self.symbol = None
-        self.display_name = self.name
-        self.LRS_score_repr = "N/A"
-        self.LRS_location_repr = "N/A"
-
-        if kw.get('fullname'):
-            name2 = value.split("::")
-            if len(name2) == 2:
-                self.dataset, self.name = name2
-
-            elif len(name2) == 3:
-                self.dataset, self.name, self.cellid = name2
-
-        # Todo: These two lines are necessary most of the time, but
-        # perhaps not all of the time So we could add a simple if
-        # statement to short-circuit this if necessary
-        if get_sample_info is not False:
-            self = retrieve_sample_data(self, self.dataset)
-
-
-def retrieve_sample_data(trait, dataset, samplelist=None):
-    if samplelist is None:
-        samplelist = []
-
-    if dataset.type == "Temp":
-        results = Redis.get(trait.name).split()
-
-    else:
-        results = dataset.retrieve_sample_data(trait.name)
-
-    # Todo: is this necessary? If not remove
-    trait.data.clear()
-
-    if results:
-        if dataset.type == "Temp":
-            all_samples_ordered = dataset.group.all_samples_ordered()
-            for i, item in enumerate(results):
-                try:
-                    trait.data[all_samples_ordered[i]] = webqtlCaseData(
-                        all_samples_ordered[i], float(item))
-
-                except Exception as e:
-                    pass
-
-
-        else:
-            for item in results:
-                name, value, variance, num_cases, name2 = item
-                if not samplelist or (samplelist and name in samplelist):
-                    trait.data[name] = webqtlCaseData(*item)
-
-    return trait
-
-def retrieve_trait_info(trait, dataset, get_qtl_info=False):
-    assert dataset, "Dataset doesn't exist"
-
-    the_url = None
-    # some code should be added  added here
-
-    try:
-        response = requests.get(the_url).content
-        trait_info = json.loads(response)
-    except:  # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
-        if dataset.type == 'Publish':
-            query = """
-                    SELECT
-                            PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
-                            CAST(Phenotype.Pre_publication_description AS BINARY),
-                            CAST(Phenotype.Post_publication_description AS BINARY),
-                            CAST(Phenotype.Original_description AS BINARY),
-                            CAST(Phenotype.Pre_publication_abbreviation AS BINARY),
-                            CAST(Phenotype.Post_publication_abbreviation AS BINARY), PublishXRef.mean,
-                            Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
-                            CAST(Publication.Authors AS BINARY), CAST(Publication.Title AS BINARY), CAST(Publication.Abstract AS BINARY),
-                            CAST(Publication.Journal AS BINARY), Publication.Volume, Publication.Pages,
-                            Publication.Month, Publication.Year, PublishXRef.Sequence,
-                            Phenotype.Units, PublishXRef.comments
-                    FROM
-                            PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
-                    WHERE
-                            PublishXRef.Id = %s AND
-                            Phenotype.Id = PublishXRef.PhenotypeId AND
-                            Publication.Id = PublishXRef.PublicationId AND
-                            PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-                            PublishXRef.InbredSetId = InbredSet.Id AND
-                            PublishFreeze.Id = %s
-                    """ % (trait.name, dataset.id)
-
-            trait_info = g.db.execute(query).fetchone()
-
-        # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
-        # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
-        elif dataset.type == 'ProbeSet':
-            display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
-            display_fields_string = 'ProbeSet.' + display_fields_string
-            query = """
-                    SELECT %s
-                    FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
-                    WHERE
-                            ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-                            ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                            ProbeSetFreeze.Name = '%s' AND
-                            ProbeSet.Name = '%s'
-                    """ % (escape(display_fields_string),
-                           escape(dataset.name),
-                           escape(str(trait.name)))
-
-            trait_info = g.db.execute(query).fetchone()
-        # XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
-        # to avoid the problem of same marker name from different species.
-        elif dataset.type == 'Geno':
-            display_fields_string = ',Geno.'.join(dataset.display_fields)
-            display_fields_string = 'Geno.' + display_fields_string
-            query = """
-                    SELECT %s
-                    FROM Geno, GenoFreeze, GenoXRef
-                    WHERE
-                            GenoXRef.GenoFreezeId = GenoFreeze.Id AND
-                            GenoXRef.GenoId = Geno.Id AND
-                            GenoFreeze.Name = '%s' AND
-                            Geno.Name = '%s'
-                    """ % (escape(display_fields_string),
-                           escape(dataset.name),
-                           escape(trait.name))
-
-            trait_info = g.db.execute(query).fetchone()
-        else:  # Temp type
-            query = """SELECT %s FROM %s WHERE Name = %s"""
-
-            trait_info = g.db.execute(query,
-                                      ','.join(dataset.display_fields),
-                                      dataset.type, trait.name).fetchone()
-
-    if trait_info:
-        trait.haveinfo = True
-        for i, field in enumerate(dataset.display_fields):
-            holder = trait_info[i]
-            if isinstance(holder, bytes):
-                holder = holder.decode("utf-8", errors="ignore")
-            setattr(trait, field, holder)
-
-        if dataset.type == 'Publish':
-            if trait.group_code:
-                trait.display_name = trait.group_code + "_" + str(trait.name)
-
-            trait.confidential = 0
-            if trait.pre_publication_description and not trait.pubmed_id:
-                trait.confidential = 1
-
-            description = trait.post_publication_description
-
-            # If the dataset is confidential and the user has access to confidential
-            # phenotype traits, then display the pre-publication description instead
-            # of the post-publication description
-            trait.description_display = ""
-            if not trait.pubmed_id:
-                trait.abbreviation = trait.pre_publication_abbreviation
-                trait.description_display = trait.pre_publication_description
-            else:
-                trait.abbreviation = trait.post_publication_abbreviation
-                if description:
-                    trait.description_display = description.strip()
-
-            if not trait.year.isdigit():
-                trait.pubmed_text = "N/A"
-            else:
-                trait.pubmed_text = trait.year
-
-            # moved to config
-
-            PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
-
-            if trait.pubmed_id:
-                trait.pubmed_link = PUBMEDLINK_URL % trait.pubmed_id
-
-        if dataset.type == 'ProbeSet' and dataset.group:
-            description_string = trait.description
-            target_string = trait.probe_target_description
-
-            if str(description_string or "") != "" and description_string != 'None':
-                description_display = description_string
-            else:
-                description_display = trait.symbol
-
-            if (str(description_display or "") != "" and
-                description_display != 'N/A' and
-                    str(target_string or "") != "" and target_string != 'None'):
-                description_display = description_display + '; ' + target_string.strip()
-
-            # Save it for the jinja2 template
-            trait.description_display = description_display
-
-            trait.location_repr = 'N/A'
-            if trait.chr and trait.mb:
-                trait.location_repr = 'Chr%s: %.6f' % (
-                    trait.chr, float(trait.mb))
-
-        elif dataset.type == "Geno":
-            trait.location_repr = 'N/A'
-            if trait.chr and trait.mb:
-                trait.location_repr = 'Chr%s: %.6f' % (
-                    trait.chr, float(trait.mb))
-
-        if get_qtl_info:
-            # LRS and its location
-            trait.LRS_score_repr = "N/A"
-            trait.LRS_location_repr = "N/A"
-            trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
-            if dataset.type == 'ProbeSet' and not trait.cellid:
-                trait.mean = ""
-                query = """
-                        SELECT
-                                ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
-                        FROM
-                                ProbeSetXRef, ProbeSet
-                        WHERE
-                                ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                                ProbeSet.Name = "{}" AND
-                                ProbeSetXRef.ProbeSetFreezeId ={}
-                        """.format(trait.name, dataset.id)
-
-                trait_qtl = g.db.execute(query).fetchone()
-                if trait_qtl:
-                    trait.locus, trait.lrs, trait.pvalue, trait.mean, trait.additive = trait_qtl
-                    if trait.locus:
-                        query = """
-                            select Geno.Chr, Geno.Mb from Geno, Species
-                            where Species.Name = '{}' and
-                            Geno.Name = '{}' and
-                            Geno.SpeciesId = Species.Id
-                            """.format(dataset.group.species, trait.locus)
-
-                        result = g.db.execute(query).fetchone()
-                        if result:
-                            trait.locus_chr = result[0]
-                            trait.locus_mb = result[1]
-                        else:
-                            trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
-                    else:
-                        trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
-
-            if dataset.type == 'Publish':
-                query = """
-                        SELECT
-                                PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive
-                        FROM
-                                PublishXRef, PublishFreeze
-                        WHERE
-                                PublishXRef.Id = %s AND
-                                PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-                                PublishFreeze.Id =%s
-                """ % (trait.name, dataset.id)
-
-                trait_qtl = g.db.execute(query).fetchone()
-                if trait_qtl:
-                    trait.locus, trait.lrs, trait.additive = trait_qtl
-                    if trait.locus:
-                        query = """
-                            select Geno.Chr, Geno.Mb from Geno, Species
-                            where Species.Name = '{}' and
-                            Geno.Name = '{}' and
-                            Geno.SpeciesId = Species.Id
-                            """.format(dataset.group.species, trait.locus)
-
-                        result = g.db.execute(query).fetchone()
-                        if result:
-                            trait.locus_chr = result[0]
-                            trait.locus_mb = result[1]
-                        else:
-                            trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
-                    else:
-                        trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
-                else:
-                    trait.locus = trait.lrs = trait.additive = ""
-            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "":
-                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
-                    trait.locus_chr, float(trait.locus_mb))
-                if str(trait.lrs or "") != "":
-                    trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
-    else:
-        raise KeyError(repr(trait.name) +
-                       ' information is not found in the database.')
-    return trait
diff --git a/gn3/base/webqtlCaseData.py b/gn3/base/webqtlCaseData.py
deleted file mode 100644
index 8395af8..0000000
--- a/gn3/base/webqtlCaseData.py
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-
-
-# uncomment below
-
-# from utility.logger import getLogger
-# logger = getLogger(__name__)
-
-# import utility.tools
-
-# utility.tools.show_settings()
-# pylint: disable-all
-
-class webqtlCaseData:
-    """one case data in one trait"""
-
-    def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
-        self.name = name
-        self.name2 = name2                  # Other name (for traits like BXD65a)
-        self.value = value                  # Trait Value
-        self.variance = variance            # Trait Variance
-        self.num_cases = num_cases          # Number of individuals/cases
-        self.extra_attributes = None
-        self.this_id = None   # Set a sane default (can't be just "id" cause that's a reserved word)
-        self.outlier = None   # Not set to True/False until later
-
-    def __repr__(self):
-        case_data_string = "<webqtlCaseData> "
-        if self.value is not None:
-            case_data_string += "value=%2.3f" % self.value
-        if self.variance is not None:
-            case_data_string += " variance=%2.3f" % self.variance
-        if self.num_cases:
-            case_data_string += " ndata=%s" % self.num_cases
-        if self.name:
-            case_data_string += " name=%s" % self.name
-        if self.name2:
-            case_data_string += " name2=%s" % self.name2
-        return case_data_string
-
-    @property
-    def class_outlier(self):
-        """Template helper"""
-        if self.outlier:
-            return "outlier"
-        return ""
-
-    @property
-    def display_value(self):
-        if self.value is not None:
-            return "%2.3f" % self.value
-        return "x"
-
-    @property
-    def display_variance(self):
-        if self.variance is not None:
-            return "%2.3f" % self.variance
-        return "x"
-
-    @property
-    def display_num_cases(self):
-        if self.num_cases is not None:
-            return "%s" % self.num_cases
-        return "x"
\ No newline at end of file