delete dataset and trait files

8 files changed, 0 insertions, 960 deletions

diff --git a/gn3/api/datasets.py b/gn3/api/datasets.py
deleted file mode 100644
index 2d13120..0000000
--- a/gn3/api/datasets.py
+++ /dev/null
@@ -1,64 +0,0 @@
-"""this module contains code for creating datasets"""
-from flask import Blueprint
-from flask import jsonify
-
-from gn3.computations.datasets import create_dataset
-from gn3.computations.datasets import get_traits_data
-from gn3.computations.datasets import get_probeset_trait_data
-
-from gn3.db_utils import database_connector
-
-
-dataset = Blueprint("dataset", __name__)
-
-
-@dataset.route("/create/<dataset_name>/")
-@dataset.route("/create/<dataset_name>/<dataset_type>")
-def create_dataset_api(dataset_name, dataset_type=None):
-    """Endpoint of creating dataset"""
-
-    new_dataset = create_dataset(
-        dataset_type=dataset_type, dataset_name=dataset_name)
-
-    results = {
-        "dataset": new_dataset
-    }
-    return jsonify(results)
-
-
-@dataset.route("/fetch_traits_data/<dataset_name>/<dataset_type>")
-def fetch_traits_data(dataset_name, dataset_type):
-    """Endpoint for fetching Trait data"""
-    # should fetch this(temp)
-    trait_sample_ids = [4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15,
-                        17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31,
-                        35, 36, 37, 39, 98, 99, 100, 103, 487, 105, 106, 110, 115,
-                        116, 117, 118, 119, 120, 919, 147,
-                        121, 40, 41, 124, 125, 128, 135, 129, 130, 131,
-                        132, 134, 138, 139, 140, 141, 142, 144,
-                        145, 148, 149, 920, 922, 2, 3, 1, 1100]
-
-    conn, _cursor = database_connector()
-    results = get_traits_data(sample_ids=trait_sample_ids, database_instance=conn,
-                              dataset_name=dataset_name, dataset_type=dataset_type)
-    conn.close()
-
-    return jsonify({"results": results})
-
-
-@dataset.route("/fetch_probeset_data/<dataset_name>")
-def fetch_probeset_data(dataset_name):
-    """Endpoint for fetching probeset trait data"""
-    trait_sample_ids = [4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15,
-                        17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31,
-                        35, 36, 37, 39, 98, 99, 100, 103, 487, 105, 106, 110, 115,
-                        116, 117, 118, 119, 120, 919, 147,
-                        121, 40, 41, 124, 125, 128, 135, 129, 130, 131,
-                        132, 134, 138, 139, 140, 141, 142, 144,
-                        145, 148, 149, 920, 922, 2, 3, 1, 1100]
-
-    conn, _cursor = database_connector()
-
-    results = get_probeset_trait_data(trait_sample_ids, conn, dataset_name)
-
-    return jsonify({"results": results})
diff --git a/gn3/api/traits.py b/gn3/api/traits.py
deleted file mode 100644
index 002a281..0000000
--- a/gn3/api/traits.py
+++ /dev/null
@@ -1,53 +0,0 @@
-"""this module contains the all endpoints for traits"""
-from unittest import mock
-
-from flask import Blueprint
-from flask import jsonify
-from flask import request
-
-from gn3.computations.traits import fetch_trait
-from gn3.computations.traits import get_trait_info_data
-from gn3.db_utils import database_connector
-
-trait = Blueprint("trait", __name__)
-
-
-@trait.route("/<string:trait_name>/<string:dataset_name>")
-def create_trait(trait_name, dataset_name):
-    """Endpoint for creating trait and fetching strain\
-    values"""
-
-    # xtodo replace the object at most this endpoint
-    # requires dataset_type,dataset_name ,dataset_id
-    trait_dataset = {
-        "name": dataset_name,
-        "id": 12,
-        "type": "ProbeSet"  # temp values
-    }
-    conn, _cursor = database_connector()
-
-    trait_results = fetch_trait(dataset=trait_dataset,
-                                trait_name=trait_name,
-                                database=conn)
-
-    conn.close()
-
-    return jsonify(trait_results)
-
-
-@trait.route("/trait_info/<string:trait_name>", methods=["POST"])
-def fetch_trait_info(trait_name):
-    """Api endpoint for fetching the trait info \
-    expects the trait and trait dataset to have\
-    been created """
-    data = request.get_json()
-
-    trait_dataset = data["trait_dataset"]
-    trait_data = data["trait"]
-    _trait_name = trait_name  # should be used as key to return results
-
-    database_instance = mock.Mock()
-
-    results = get_trait_info_data(trait_dataset, trait_data, database_instance)
-
-    return jsonify(results)
diff --git a/gn3/computations/datasets.py b/gn3/computations/datasets.py
deleted file mode 100644
index b69583e..0000000
--- a/gn3/computations/datasets.py
+++ /dev/null
@@ -1,371 +0,0 @@
-"""module contains the code all related to datasets"""
-import json
-from math import ceil
-from collections import defaultdict
-
-from typing import Optional
-from typing import List
-
-from dataclasses import dataclass
-from MySQLdb import escape_string  # type: ignore
-
-import requests
-from gn3.settings import GN2_BASE_URL
-
-
-def retrieve_trait_sample_data(dataset,
-                               trait_name: str,
-                               database,
-                               group_species_id=None) -> List:
-    """given the dataset id and trait_name fetch the\
-    sample_name,value from the dataset"""
-
-    # should pass the db as arg all  do a setup
-
-    (dataset_name, dataset_id, dataset_type) = (dataset.get("name"), dataset.get(
-        "id"), dataset.get("type"))
-
-    dataset_query = get_query_for_dataset_sample(dataset_type)
-    results = []
-    sample_query_values = {
-        "Publish": (trait_name, dataset_id),
-        "Geno": (group_species_id, trait_name, dataset_name),
-        "ProbeSet": (trait_name, dataset_name)
-    }
-
-    if dataset_query:
-        formatted_query = dataset_query % sample_query_values[dataset_type]
-
-        results = fetch_from_db_sample_data(formatted_query, database)
-
-    return results
-
-
-def fetch_from_db_sample_data(formatted_query: str, database_instance) -> List:
-    """this is the function that does the actual fetching of\
-    results from the database"""
-    try:
-        cursor = database_instance.cursor()
-        cursor.execute(formatted_query)
-        results = cursor.fetchall()
-
-    except Exception as error:
-        raise error
-
-    cursor.close()
-
-    return results
-
-
-def get_query_for_dataset_sample(dataset_type) -> Optional[str]:
-    """this functions contains querys for\
-    getting sample data from the db depending in
-    dataset"""
-    dataset_query = {}
-
-    pheno_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
-                """
-    geno_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
-                """
-
-    probeset_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
-                """
-
-    dataset_query["Publish"] = pheno_query
-    dataset_query["Geno"] = geno_query
-    dataset_query["ProbeSet"] = probeset_query
-
-    return dataset_query.get(dataset_type)
-
-
-@dataclass
-class Dataset:
-    """class for creating datasets"""
-    name: Optional[str] = None
-    dataset_type: Optional[str] = None
-    dataset_id: int = -1
-
-
-def create_mrna_tissue_dataset(dataset_name, dataset_type):
-    """an mrna assay is a quantitative assessment(assay) associated\
-    with an mrna trait.This used to be called probeset,but that term\
-    only referes specifically to the afffymetrix platform and is\
-    far too speficified"""
-
-    return Dataset(name=dataset_name, dataset_type=dataset_type)
-
-
-def dataset_type_getter(dataset_name, redis_instance=None) -> Optional[str]:
-    """given the dataset name fetch the type\
-    of the dataset this in turn  enables fetching\
-    the creation of the correct object could utilize\
-    redis for the case"""
-
-    results = redis_instance.get(dataset_name, None)
-
-    if results:
-        return results
-
-    return fetch_dataset_type_from_gn2_api(dataset_name)
-
-
-def fetch_dataset_type_from_gn2_api(dataset_name):
-    """this function is only called when the\
-    the redis is empty and does have the specificied\
-    dataset_type"""
-    # should only run once
-
-    dataset_structure = {}
-
-    map_dataset_to_new_type = {
-        "Phenotypes": "Publish",
-        "Genotypes": "Geno",
-        "MrnaTypes": "ProbeSet"
-    }
-
-    data = json.loads(requests.get(
-        GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content)
-    _name = dataset_name
-    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]:
-                    # assumes  the first is dataset_short_name
-                    short_dataset_name = next(
-                        item for item in dataset if item != "None" and item is not None)
-
-                    dataset_structure[short_dataset_name] = map_dataset_to_new_type.get(
-                        dataset_type, "MrnaTypes")
-    return dataset_structure
-
-
-def dataset_creator_store(dataset_type):
-    """function contains key value pairs for\
-    the function need to be called to create\
-    each dataset_type"""
-
-    dataset_obj = {
-        "ProbeSet": create_mrna_tissue_dataset
-    }
-
-    return dataset_obj[dataset_type]
-
-
-def create_dataset(dataset_type=None, dataset_name: str = None):
-    """function for creating new dataset  temp not implemented"""
-    if dataset_type is None:
-        dataset_type = dataset_type_getter(dataset_name)
-
-    dataset_creator = dataset_creator_store(dataset_type)
-    results = dataset_creator(
-        dataset_name=dataset_name, dataset_type=dataset_type)
-    return results
-
-
-def fetch_dataset_sample_id(samplelist: List, database, species: str) -> dict:
-    """fetch the strain ids from the db only if\
-    it is in the samplelist"""
-    # xtodo create an in clause for samplelist
-
-    strain_query = """
-        SELECT Strain.Name, Strain.Id FROM Strain, Species
-        WHERE Strain.Name IN {}
-        and Strain.SpeciesId=Species.Id
-        and Species.name = '{}'
-        """
-
-    database_cursor = database.cursor()
-    database_cursor.execute(strain_query.format(samplelist, species))
-
-    results = database_cursor.fetchall()
-
-    return dict(results)
-
-
-def divide_into_chunks(the_list, number_chunks):
-    """Divides a list into approximately number_chunks
-    >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3)
-    [[1, 2, 7], [3, 22, 8], [5, 22, 333]]"""
-
-    length = len(the_list)
-    if length == 0:
-        return [[]]
-
-    if length <= number_chunks:
-        number_chunks = length
-    chunk_size = int(ceil(length/number_chunks))
-    chunks = []
-
-    for counter in range(0, length, chunk_size):
-        chunks.append(the_list[counter:counter+chunk_size])
-    return chunks
-
-
-def escape(string_):
-    """function escape sql value"""
-    return escape_string(string_).decode('utf8')
-
-
-def mescape(*items) -> List:
-    """multiple escape for query values"""
-
-    return [escape_string(str(item)).decode('utf8') for item in items]
-
-
-def get_traits_data(sample_ids, database_instance, dataset_name, dataset_type):
-    """function to fetch trait data"""
-    # 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
-
-    _trait_data = defaultdict(list)
-    chunk_size = 61
-    number_chunks = int(ceil(len(sample_ids) / chunk_size))
-    for sample_ids_step in divide_into_chunks(sample_ids, number_chunks):
-        if dataset_type == "Publish":
-            full_dataset_type = "Phenotype"
-        else:
-            full_dataset_type = dataset_type
-        temp = ['T%s.value' % item for item in sample_ids_step]
-
-        if dataset_type == "Publish":
-            query = "SELECT {}XRef.Id,".format(escape(dataset_type))
-
-        else:
-            query = "SELECT {}.Name,".format(escape(full_dataset_type))
-
-        query += ', '.join(temp)
-        query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(full_dataset_type,
-                                                                 dataset_type,
-                                                                 dataset_type))
-        for item in sample_ids_step:
-
-            query += """
-                    left join {}Data as T{} on T{}.Id = {}XRef.DataId
-                    and T{}.StrainId={}\n
-                    """.format(*mescape(dataset_type, item,
-                                        item, dataset_type, item, item))
-
-        if dataset_type == "Publish":
-            query += """
-                        WHERE {}XRef.{}FreezeId = {}Freeze.Id
-                        and {}Freeze.Name = '{}'
-                        and {}.Id = {}XRef.{}Id
-                        order by {}.Id
-                        """.format(*mescape(dataset_type, dataset_type,
-                                            dataset_type, dataset_type,
-                                            dataset_name, full_dataset_type,
-                                            dataset_type, dataset_type,
-                                            full_dataset_type))
-
-        else:
-            query += """
-                        WHERE {}XRef.{}FreezeId = {}Freeze.Id
-                        and {}Freeze.Name = '{}'
-                        and {}.Id = {}XRef.{}Id
-                        order by {}.Id
-                        """.format(*mescape(dataset_type, dataset_type,
-                                            dataset_type, dataset_type,
-                                            dataset_name, dataset_type,
-                                            dataset_type, dataset_type,
-                                            full_dataset_type))
-
-        # print(query)
-
-        _results = fetch_from_db_sample_data(query, database_instance)
-
-        return []
-
-
-def get_probeset_trait_data(strain_ids: List, conn, dataset_name) -> dict:
-    """function for getting trait data\
-    for probeset data type similar to\
-    get trait data only difference is that\
-    it uses sub queries"""
-
-    trait_data: dict = {}
-
-    trait_id_name = {}
-
-    traits_query = """
-    SELECT ProbeSetXRef.DataId,ProbeSet.Name FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
-                    WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
-                    and ProbeSetFreeze.Name = '{}'
-                    and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-                    order by ProbeSet.Id
-    """.format(dataset_name)
-
-    query = """
-    SELECT * from ProbeSetData
-    where StrainID in ({})
-    and id in (SELECT ProbeSetXRef.DataId FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
-                WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
-                and ProbeSetFreeze.Name = '{}'
-                and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-                order by ProbeSet.Id)
-    """.format(",".join(str(strain_id) for strain_id in strain_ids), dataset_name)
-
-    with conn:
-        cursor = conn.cursor()
-        cursor.execute(query)
-        _results = cursor.fetchall()
-        cursor.execute(traits_query)
-        trait_id_name = dict(cursor.fetchall())
-
-    for trait_id, _strain_id, strain_value in _results:
-        trait_name = trait_id_name[trait_id]
-        if trait_data.get(trait_name):
-            trait_data[trait_name].append(strain_value)
-        else:
-            trait_data[trait_name] = []
-
-            trait_data[trait_name].append(strain_value)
-
-    return trait_data
diff --git a/gn3/computations/traits.py b/gn3/computations/traits.py
deleted file mode 100644
index 1aa2970..0000000
--- a/gn3/computations/traits.py
+++ /dev/null
@@ -1,56 +0,0 @@
-"""module contains all operating related to traits"""
-from gn3.computations.datasets import retrieve_trait_sample_data
-
-
-def fetch_trait(dataset, trait_name: str, database) -> dict:
-    """this method creates a trait by\
-    fetching required data given the\
-    dataset and trait_name"""
-
-    created_trait = {
-        "dataset": dataset,
-        "trait_name": trait_name
-    }
-
-    trait_data = get_trait_sample_data(dataset, trait_name, database)
-
-    created_trait["trait_data"] = trait_data
-
-    return created_trait
-
-
-def get_trait_sample_data(trait_dataset, trait_name, database) -> dict:
-    """first try to fetch the traits sample data from redis if that\
-    try to fetch from the traits dataset redis is only  used for\
-    temp dataset type which is not used in this case """
-
-    sample_results = retrieve_trait_sample_data(
-        trait_dataset, trait_name, database)
-
-    trait_data = {}
-
-    for (name, sample_value, _variance, _numcase, _name2) in sample_results:
-
-        trait_data[name] = sample_value
-    return trait_data
-
-
-def get_trait_info_data(trait_dataset,
-                        trait_name: str,
-                        database_instance,
-                        get_qtl_info: bool = False) -> dict:
-    """given a dataset and trait_name return a dict containing all info\
-    regarding the get trait"""
-
-    _temp_var_holder = (trait_dataset, trait_name,
-                        database_instance, get_qtl_info)
-    trait_info_data = {
-        "description": "",
-        "chr": "",
-        "locus": "",
-        "mb": "",
-        "abbreviation": "",
-        "trait_display_name": ""
-
-    }
-    return trait_info_data
diff --git a/tests/integration/test_datasets.py b/tests/integration/test_datasets.py
deleted file mode 100644
index f97d970..0000000
--- a/tests/integration/test_datasets.py
+++ /dev/null
@@ -1,41 +0,0 @@
-"""This module contains integration tests for datasets"""
-from unittest import TestCase
-from unittest import mock
-
-from collections import namedtuple
-from gn3.app import create_app
-
-
-class DatasetIntegrationTests(TestCase):
-    """class contains integration tests for datasets"""
-
-    def setUp(self):
-        self.app = create_app().test_client()
-
-    @mock.patch("gn3.api.datasets.create_dataset")
-    def test_create_dataset(self, mock_dataset):
-        """Test for creating dataset object"""
-        mock_dataset_creator = namedtuple(
-            'ProbeSet', ["dataset_name", "dataset_type"])
-        new_dataset = mock_dataset_creator("HC_M2_0606_P", "ProbeSet")
-        mock_dataset.return_value = new_dataset
-        response = self.app.get(
-            "/api/dataset/create/HC_M2_0606_P/", follow_redirects=True)
-        mock_dataset.assert_called_once_with(
-            dataset_type=None, dataset_name="HC_M2_0606_P")
-        results = response.get_json()["dataset"]
-        self.assertEqual(results[1], "ProbeSet")
-        self.assertEqual(response.status_code, 200)
-
-    @mock.patch("gn3.api.datasets.get_traits_data")
-    @mock.patch("gn3.api.datasets.database_connector")
-    def test_fetch_traits_data(self, mock_db, mock_get_trait_data):
-        """Test api/dataset/fetch_traits_data/d_name/d_type"""
-
-        mock_get_trait_data.return_value = {}
-        mock_db.return_value = (mock.Mock(), mock.Mock())
-        response = self.app.get(
-            "/api/dataset/fetch_traits_data/Aging-Brain-UCIPublish/Publish", follow_redirects=True)
-
-        self.assertEqual(response.status_code, 200)
-        self.assertEqual(response.get_json(), {"results": {}})
diff --git a/tests/integration/test_traits.py b/tests/integration/test_traits.py
deleted file mode 100644
index 410ba22..0000000
--- a/tests/integration/test_traits.py
+++ /dev/null
@@ -1,72 +0,0 @@
-"""module contains integration tests for trait endpoints"""
-from unittest import TestCase
-from unittest import mock
-
-from gn3.app import create_app
-
-
-class TraitIntegrationTest(TestCase):
-    """class contains integration tests for\
-    traits"""
-
-    def setUp(self):
-        self.app = create_app().test_client()
-
-    @mock.patch("gn3.api.traits.fetch_trait")
-    @mock.patch("gn3.api.traits.database_connector")
-    def test_create_trait(self, mock_database, mock_fetch_trait):
-        """test the endpoint for creating traits\
-        endpoint requires trait name and dataset name"""
-        mock_database.return_value = (mock.Mock(), mock.Mock())
-        trait_results = {
-            "dataset": None,
-            "trait_name": "1449593_at",
-            "trait_data": {
-                "BXD11": 8.464,
-                "BXD12": 8.414,
-                "BXD13": 8.753,
-                "BXD15": 8.5,
-                "BXD16": 8.832
-            }
-
-        }
-        mock_fetch_trait.return_value = trait_results
-
-        results = self.app.get(
-            "/api/trait/1449593_at/HC_M2_0606_P", follow_redirects=True)
-
-        trait_data = results.get_json()
-
-        self.assertEqual(mock_database.call_count, 1)
-        self.assertEqual(results.status_code, 200)
-        self.assertEqual(trait_data, trait_results)
-
-    @mock.patch("gn3.api.traits.get_trait_info_data")
-    def test_retrieve_trait_info(self, mock_get_trait_info):
-        """integration test for endpoints for retrieving\
-        trait info expects the dataset of trait to have been
-        created"""
-
-        trait_post_data = {
-            "trait": {"trait_name": ""},
-            "trait_dataset": {"dataset_name": ""}
-        }
-
-        expected_api_results = {
-            "description": "trait description",
-            "chr": "",
-            "locus": "",
-            "mb": "",
-            "abbreviation": "trait_abbreviation",
-            "trait_display_name": "trait_name"
-
-        }
-        mock_get_trait_info.return_value = expected_api_results
-
-        trait_info = self.app.post(
-            "/api/trait/trait_info/144_at", json=trait_post_data, follow_redirects=True)
-
-        trait_info_results = trait_info.get_json()
-
-        self.assertEqual(trait_info.status_code, 200)
-        self.assertEqual(trait_info_results, expected_api_results)
diff --git a/tests/unit/computations/test_datasets.py b/tests/unit/computations/test_datasets.py
deleted file mode 100644
index f9e9c2b..0000000
--- a/tests/unit/computations/test_datasets.py
+++ /dev/null
@@ -1,219 +0,0 @@
-"""Module contains tests from datasets"""
-import json
-
-from unittest import TestCase
-from unittest import mock
-
-from collections import namedtuple
-
-from gn3.computations.datasets import retrieve_trait_sample_data
-from gn3.computations.datasets import get_query_for_dataset_sample
-from gn3.computations.datasets import fetch_from_db_sample_data
-from gn3.computations.datasets import create_dataset
-from gn3.computations.datasets import dataset_creator_store
-from gn3.computations.datasets import dataset_type_getter
-from gn3.computations.datasets import fetch_dataset_type_from_gn2_api
-from gn3.computations.datasets import fetch_dataset_sample_id
-from gn3.computations.datasets import divide_into_chunks
-from gn3.computations.datasets import get_traits_data
-
-
-class TestDatasets(TestCase):
-    """Class contains tests for datasets"""
-
-    @mock.patch("gn3.computations.datasets.fetch_from_db_sample_data")
-    def test_retrieve_trait_sample_data(self, mock_fetch_sample_results):
-        """Test  retrieving sample data\
-         for trait from the dataset
-        """
-        trait_name = "1419792_at"
-        dataset_id = "HC_M2_0606_P&"
-        dataset_type = "Publish"
-
-        database = mock.Mock()
-
-        dataset = {
-            "id": dataset_id,
-            "type": dataset_type,
-            "name": dataset_id
-        }
-
-        fetch_results = [('BXD32', 8.001, None, None, 'BXD32')]
-
-        mock_fetch_sample_results.return_value = fetch_results
-
-        results = retrieve_trait_sample_data(
-            dataset, trait_name, database)
-        self.assertEqual(mock_fetch_sample_results.call_count, 1)
-        self.assertEqual(results, fetch_results)
-
-    def test_query_for_dataset_sample(self):
-        """Test for getting query for sample data"""
-
-        no_results = get_query_for_dataset_sample("does not exists")
-
-        query_exists = get_query_for_dataset_sample("Publish")
-
-        self.assertEqual(no_results, None)
-        self.assertIsInstance(query_exists, str)
-
-    def test_fetch_from_db_sample_data(self):
-        """Test for function that fetches sample\
-        results from the database
-        """
-
-        database_results = [('BXD31', 8.001, None, None, 'BXD31'),
-                            ('BXD32', 7.884, None, None, 'BXD32'),
-                            ('BXD42', 7.682, None, None, 'BXD42'),
-                            ('BXD42', 7.682, None, None, 'BXD42'),
-                            ('BXD40', 7.945, None, None, 'BXD40'),
-                            ('BXD43', 7.873, None, None, 'BXD43')
-                            ]
-
-        database = mock.Mock()
-        db_cursor = mock.Mock()
-        db_cursor.execute.return_value = 6
-        db_cursor.fetchall.return_value = database_results
-        database.cursor.return_value = db_cursor
-
-        mock_pheno_query = """
-                    SELECT
-                            Strain.Name, PublishData.value, PublishSE.error,NStrain.count, Strain.Name2
-                    WHERE
-                            PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-                            PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = 1419792_at AND
-                            PublishFreeze.Id = '12' AND PublishData.StrainId = Strain.Id
-                    Order BY
-                            Strain.Name
-                    """
-        fetch_results = fetch_from_db_sample_data(mock_pheno_query, database)
-
-        self.assertEqual(fetch_results, database_results)
-
-    @mock.patch("gn3.computations.datasets.dataset_creator_store")
-    @mock.patch("gn3.computations.datasets.dataset_type_getter")
-    def test_create_dataset(self, mock_dataset_type, mock_store):
-        """Test function that creates/fetches required dataset\
-        can either be published phenotype,genotype,Microarray or\
-        user defined ->Temp
-        """
-        probe_name = "HC_M2_0606_P"
-        probe_type = "ProbeSet"
-
-        mock_dataset_creator = namedtuple(
-            'ProbeSet', ["dataset_name", "dataset_type"])
-
-        mock_store.return_value = mock_dataset_creator
-        mock_dataset_type.return_value = probe_type
-        dataset = create_dataset(
-            dataset_type=None, dataset_name=probe_name)
-
-        self.assertEqual(dataset.dataset_name, probe_name)
-        self.assertEqual(dataset.dataset_type, probe_type)
-
-    def test_dataset_creator_store(self):
-        """Test  for functions that actual
-        function to create differerent \
-        datasets
-        """
-        results = dataset_creator_store("ProbeSet")
-
-        self.assertTrue(results)
-
-    def test_dataset_type_getter(self):
-        """Test for fetching type of dataset given\
-        the dataset name
-        """
-
-        redis_instance = mock.Mock()
-        # fetched  in redis
-        redis_instance.get.return_value = "ProbeSet"
-        results = dataset_type_getter("HC_M2_0_P", redis_instance)
-        self.assertEqual(results, "ProbeSet")
-
-    @mock.patch("gn3.computations.datasets.requests")
-    def test_fetch_dataset_type_from_gn2_api(self, mock_request):
-        """Test for function that test fetching\
-        all datasets from gn2 api in order to store\
-        in redis
-        """
-
-        expected_json_results = {"datasets": {
-            "arabidopsis": {
-                "BayXSha": {
-                    "Genotypes": [
-                        [
-                            "None",
-                            "BayXShaGeno",
-                            "BayXSha Genotypes"
-                        ]
-                    ],
-                    "Phenotypes": [
-                        [
-                            "642",
-                            "BayXShaPublish",
-                            "BayXSha Published Phenotypes"
-                        ]
-                    ]
-                }
-            }
-        }}
-
-        request_results = json.dumps(expected_json_results)
-        mock_request.get.return_value.content = request_results
-        results = fetch_dataset_type_from_gn2_api("HC_M2_0_P")
-        expected_results = {
-            "BayXShaGeno": "Geno",
-            "642": "Publish"
-        }
-
-        self.assertEqual(expected_results, results)
-
-    def test_fetch_dataset_sample_id(self):
-        """Get from the database the sample\
-        id if only in the samplelists
-        """
-
-        expected_results = {"B6D2F1": 1, "BXD1": 4, "BXD11": 10,
-                            "BXD12": 11, "BXD13": 12, "BXD15": 14, "BXD16": 15}
-
-        database_instance = mock.Mock()
-        database_cursor = mock.Mock()
-
-        database_cursor.execute.return_value = 5
-        database_cursor.fetchall.return_value = list(expected_results.items())
-        database_instance.cursor.return_value = database_cursor
-        strain_list = ["B6D2F1", "BXD1", "BXD11",
-                       "BXD12", "BXD13", "BXD16", "BXD15"]
-
-        results = fetch_dataset_sample_id(
-            samplelist=strain_list, database=database_instance, species="mouse")
-
-        self.assertEqual(results, expected_results)
-
-    @mock.patch("gn3.computations.datasets.fetch_from_db_sample_data")
-    @mock.patch("gn3.computations.datasets.divide_into_chunks")
-    def test_get_traits_data(self, mock_divide_into_chunks, mock_fetch_samples):
-        """Test for for function to get data\
-        of traits in dataset
-        """
-        _expected_results = {'AT_DSAFDS': [
-            12, 14, 13, 23, 12, 14, 13, 23, 12, 14, 13, 23]}
-        database = mock.Mock()
-        sample_id = [1, 2, 7, 3, 22, 8]
-        mock_divide_into_chunks.return_value = [
-            [1, 2, 7], [3, 22, 8], [5, 22, 333]]
-        mock_fetch_samples.return_value = ("AT_DSAFDS", 12, 14, 13, 23)
-        results = get_traits_data(sample_id, database, "HC_M2", "Publish")
-
-        self.assertEqual({}, dict(results))
-
-    def test_divide_into_chunks(self):
-        """Test for dividing a list into given number of\
-        chunks for example
-        """
-        results = divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3)
-
-        expected_results = [[1, 2, 7], [3, 22, 8], [5, 22, 333]]
-
-        self.assertEqual(results, expected_results)
diff --git a/tests/unit/computations/test_trait.py b/tests/unit/computations/test_trait.py
deleted file mode 100644
index feb97c6..0000000
--- a/tests/unit/computations/test_trait.py
+++ /dev/null
@@ -1,84 +0,0 @@
-"""Module contains tests for creating traits"""
-from unittest import TestCase
-from unittest import mock
-
-from gn3.computations.traits import fetch_trait
-from gn3.computations.traits import get_trait_sample_data
-from gn3.computations.traits import get_trait_info_data
-
-
-class TestTrait(TestCase):
-    """Class contains tests for creating traits"""
-
-    @mock.patch("gn3.computations.traits.get_trait_sample_data")
-    def test_fetch_trait(self, get_sample_data):
-        """Test for creating/fetching trait"""
-
-        expected_sample_data = {
-            "A/Y": 12.3,
-            "WQC": 11.1
-        }
-
-        database = mock.Mock()
-
-        get_sample_data.return_value = expected_sample_data
-
-        expected_trait = {
-            "trait_name": "AXFDSF_AT",
-            "dataset": None,
-            "trait_data": expected_sample_data
-        }
-        results = fetch_trait(dataset=None,
-                              trait_name="AXFDSF_AT",
-                              database=database)
-
-        self.assertEqual(results, expected_trait)
-        self.assertEqual(get_sample_data.call_count, 1)
-
-    @mock.patch("gn3.computations.traits.retrieve_trait_sample_data")
-    def test_get_trait_sample_data(self, mock_retrieve_sample_data):
-        """Test for getting sample data from  either\
-        the trait's dataset or form redis
-        """
-
-        trait_dataset = mock.Mock()
-        dataset_trait_sample_data = [
-            ('129S1/SvImJ', 7.433, None, None, '129S1/SvImJ'),
-            ('A/J', 7.596, None, None, 'A/J'),
-            ('AKR/J', 7.774, None, None, 'AKR/J'),
-            ('B6D2F1', 7.707, None, None, 'B6D2F1')]
-        mock_retrieve_sample_data.return_value = dataset_trait_sample_data
-
-        trait_name = "1426679_at"
-
-        database = mock.Mock()
-
-        results = get_trait_sample_data(
-            trait_dataset, trait_name, database)
-
-        expected_results = {
-            "129S1/SvImJ": 7.433,
-            "A/J": 7.596,
-            "AKR/J": 7.774,
-            "B6D2F1": 7.707
-        }
-
-        self.assertEqual(results, expected_results)
-
-    def test_get_trait_info_data(self):
-        """Test for getting info data related\
-        to trait
-        """
-
-        results = get_trait_info_data(
-            trait_name="AXSF_AT", trait_dataset=mock.Mock(), database_instance=None)
-        expected_trait_info = {
-            "description": "",
-            "trait_display_name": "",
-            "abbreviation": "",
-            "chr": "",
-            "mb": "",
-            "locus": ""
-        }
-
-        self.assertEqual(results, expected_trait_info)