Merge branch 'partial-correlations'

35 files changed, 4101 insertions, 531 deletions

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 926b054..e9a2425 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,3 +1,5 @@
+Please fill out the template below, and delete items not applicable to your pull request.
+
 #### Description
 <!--Brief description of the PR. What does this PR do? -->
 
diff --git a/README.md b/README.md
index 84a7a54..62e8aeb 100644
--- a/README.md
+++ b/README.md
@@ -9,8 +9,8 @@ Install GNU Guix - this can be done on every running Linux system.
 
 There are at least three ways to start GeneNetwork3 with GNU Guix:
 
-1. Create an environment with `guix environment`
-2. Create a container with `guix environment -C`
+1. Create an environment with `guix shell`
+2. Create a container with `guix shell -C`
 3. Use a profile and shell settings with `source ~/opt/genenetwork3/etc/profile`
 
 #### Create an environment:
@@ -18,13 +18,13 @@ There are at least three ways to start GeneNetwork3 with GNU Guix:
 Simply load up the environment (for development purposes):
 
 ```bash
-guix environment --load=guix.scm
+guix shell -Df guix.scm
 ```
 
 Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up.
 
 ```bash
-env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --expose=$HOME/genotype_files/ --load=guix.scm
+guix shell --expose=$HOME/genotype_files/ -Df guix.scm
 python3
   import redis
 ```
@@ -32,7 +32,7 @@ python3
 #### Run a Guix container
 
 ```
-env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --expose=$HOME/genotype_files/ --load=guix.scm
+guix shell -C --network --expose=$HOME/genotype_files/ -Df guix.scm
 ```
 
 
@@ -41,7 +41,7 @@ env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix env
 Create a new profile with
 
 ```
-env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix package -i genenetwork3 -p ~/opt/genenetwork3
+guix package -i genenetwork3 -p ~/opt/genenetwork3
 ```
 
 and load the profile settings with
diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py
index 62ca2ad..633a061 100644
--- a/gn3/api/heatmaps.py
+++ b/gn3/api/heatmaps.py
@@ -17,7 +17,9 @@ def clustered_heatmaps():
     Parses the incoming data and responds with the JSON-serialized plotly figure
     representing the clustered heatmap.
     """
-    traits_names = request.get_json().get("traits_names", tuple())
+    heatmap_request = request.get_json()
+    traits_names = heatmap_request.get("traits_names", tuple())
+    vertical = heatmap_request.get("vertical", False)
     if len(traits_names) < 2:
         return jsonify({
             "message": "You need to provide at least two trait names."
@@ -30,7 +32,7 @@ def clustered_heatmaps():
     traits_fullnames = [parse_trait_fullname(trait) for trait in traits_names]
 
     with io.StringIO() as io_str:
-        _filename, figure = build_heatmap(traits_fullnames, conn)
+        figure = build_heatmap(traits_fullnames, conn, vertical=vertical)
         figure.write_json(io_str)
         fig_json = io_str.getvalue()
     return fig_json, 200
diff --git a/gn3/app.py b/gn3/app.py
index a25332c..3d68b3f 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -21,12 +21,6 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
     # Load default configuration
     app.config.from_object("gn3.settings")
 
-    CORS(
-        app,
-        origins=app.config["CORS_ORIGINS"],
-        allow_headers=app.config["CORS_HEADERS"],
-        supports_credentials=True, intercept_exceptions=False)
-
     # Load environment configuration
     if "GN3_CONF" in os.environ:
         app.config.from_envvar('GN3_CONF')
@@ -37,6 +31,13 @@ def create_app(config: Union[Dict, str, None] = None) -> Flask:
             app.config.update(config)
         elif config.endswith(".py"):
             app.config.from_pyfile(config)
+
+    CORS(
+        app,
+        origins=app.config["CORS_ORIGINS"],
+        allow_headers=app.config["CORS_HEADERS"],
+        supports_credentials=True, intercept_exceptions=False)
+
     app.register_blueprint(general, url_prefix="/api/")
     app.register_blueprint(gemma, url_prefix="/api/gemma")
     app.register_blueprint(rqtl, url_prefix="/api/rqtl")
diff --git a/gn3/authentication.py b/gn3/authentication.py
new file mode 100644
index 0000000..a6372c1
--- /dev/null
+++ b/gn3/authentication.py
@@ -0,0 +1,165 @@
+"""Methods for interacting with gn-proxy."""
+import functools
+import json
+import uuid
+import datetime
+
+from urllib.parse import urljoin
+from enum import Enum, unique
+from typing import Dict, List, Optional, Union
+
+from redis import Redis
+import requests
+
+
+@functools.total_ordering
+class OrderedEnum(Enum):
+    """A class that ordered Enums in order of position"""
+    @classmethod
+    @functools.lru_cache(None)
+    def _member_list(cls):
+        return list(cls)
+
+    def __lt__(self, other):
+        if self.__class__ is other.__class__:
+            member_list = self.__class__._member_list()
+            return member_list.index(self) < member_list.index(other)
+        return NotImplemented
+
+
+@unique
+class DataRole(OrderedEnum):
+    """Enums for Data Access"""
+    NO_ACCESS = "no-access"
+    VIEW = "view"
+    EDIT = "edit"
+
+
+@unique
+class AdminRole(OrderedEnum):
+    """Enums for Admin status"""
+    NOT_ADMIN = "not-admin"
+    EDIT_ACCESS = "edit-access"
+    EDIT_ADMINS = "edit-admins"
+
+
+def get_user_membership(conn: Redis, user_id: str,
+                        group_id: str) -> Dict:
+    """Return a dictionary that indicates whether the `user_id` is a
+    member or admin of `group_id`.
+
+    Args:
+      - conn: a Redis Connection with the responses decoded.
+      - user_id: a user's unique id
+        e.g. '8ad942fe-490d-453e-bd37-56f252e41603'
+      - group_id: a group's unique id
+      e.g. '7fa95d07-0e2d-4bc5-b47c-448fdc1260b2'
+
+    Returns:
+      A dict indicating whether the user is an admin or a member of
+      the group: {"member": True, "admin": False}
+
+    """
+    results = {"member": False, "admin": False}
+    for key, value in conn.hgetall('groups').items():
+        if key == group_id:
+            group_info = json.loads(value)
+            if user_id in group_info.get("admins"):
+                results["admin"] = True
+            if user_id in group_info.get("members"):
+                results["member"] = True
+            break
+    return results
+
+
+def get_highest_user_access_role(
+        resource_id: str,
+        user_id: str,
+        gn_proxy_url: str = "http://localhost:8080") -> Dict:
+    """Get the highest access roles for a given user
+
+    Args:
+      - resource_id: The unique id of a given resource.
+      - user_id: The unique id of a given user.
+      - gn_proxy_url: The URL where gn-proxy is running.
+
+    Returns:
+      A dict indicating the highest access role the user has.
+
+    """
+    role_mapping: Dict[str, Union[DataRole, AdminRole]] = {}
+    for data_role, admin_role in zip(DataRole, AdminRole):
+        role_mapping.update({data_role.value: data_role, })
+        role_mapping.update({admin_role.value: admin_role, })
+    access_role = {}
+    response = requests.get(urljoin(gn_proxy_url,
+                                    ("available?resource="
+                                     f"{resource_id}&user={user_id}")))
+    for key, value in json.loads(response.content).items():
+        access_role[key] = max(map(lambda role: role_mapping[role], value))
+    return access_role
+
+
+def get_groups_by_user_uid(user_uid: str, conn: Redis) -> Dict:
+    """Given a user uid, get the groups in which they are a member or admin of.
+
+    Args:
+      - user_uid: A user's unique id
+      - conn: A redis connection
+
+    Returns:
+      - A dictionary containing the list of groups the user is part of e.g.:
+        {"admin": [], "member": ["ce0dddd1-6c50-4587-9eec-6c687a54ad86"]}
+    """
+    admin = []
+    member = []
+    for group_uuid, group_info in conn.hgetall("groups").items():
+        group_info = json.loads(group_info)
+        group_info["uuid"] = group_uuid
+        if user_uid in group_info.get('admins'):
+            admin.append(group_info)
+        if user_uid in group_info.get('members'):
+            member.append(group_info)
+    return {
+        "admin": admin,
+        "member": member,
+    }
+
+
+def get_user_info_by_key(key: str, value: str,
+                         conn: Redis) -> Optional[Dict]:
+    """Given a key, get a user's information if value is matched"""
+    if key != "user_id":
+        for user_uuid, user_info in conn.hgetall("users").items():
+            user_info = json.loads(user_info)
+            if (key in user_info and user_info.get(key) == value):
+                user_info["user_id"] = user_uuid
+                return user_info
+    elif key == "user_id":
+        if user_info := conn.hget("users", value):
+            user_info = json.loads(user_info)
+            user_info["user_id"] = value
+            return user_info
+    return None
+
+
+def create_group(conn: Redis, group_name: Optional[str],
+                 admin_user_uids: List = None,
+                 member_user_uids: List = None) -> Optional[Dict]:
+    """Create a group given the group name, members and admins of that group."""
+    if admin_user_uids is None:
+        admin_user_uids = []
+    if member_user_uids is None:
+        member_user_uids = []
+    if group_name and bool(admin_user_uids + member_user_uids):
+        timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        group = {
+            "id": (group_id := str(uuid.uuid4())),
+            "admins": admin_user_uids,
+            "members": member_user_uids,
+            "name": group_name,
+            "created_timestamp": timestamp,
+            "changed_timestamp": timestamp,
+        }
+        conn.hset("groups", group_id, json.dumps(group))
+        return group
diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py
deleted file mode 100644
index 7accd0c..0000000
--- a/gn3/computations/biweight.py
+++ /dev/null
@@ -1,27 +0,0 @@
-"""module contains script to call biweight midcorrelation in R"""
-import subprocess
-
-from typing import List
-from typing import Tuple
-
-from gn3.settings import BIWEIGHT_RSCRIPT
-
-
-def calculate_biweight_corr(trait_vals: List,
-                            target_vals: List,
-                            path_to_script: str = BIWEIGHT_RSCRIPT,
-                            command: str = "Rscript"
-                            ) -> Tuple[float, float]:
-    """biweight function"""
-
-    args_1 = ' '.join(str(trait_val) for trait_val in trait_vals)
-    args_2 = ' '.join(str(target_val) for target_val in target_vals)
-    cmd = [command, path_to_script] + [args_1] + [args_2]
-
-    results = subprocess.check_output(cmd, universal_newlines=True)
-    try:
-        (corr_coeff, p_val) = tuple(
-            [float(y.strip()) for y in results.split()])
-        return (corr_coeff, p_val)
-    except Exception as error:
-        raise error
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index bb13ff1..c5c56db 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -1,6 +1,7 @@
 """module contains code for correlations"""
 import math
 import multiprocessing
+from contextlib import closing
 
 from typing import List
 from typing import Tuple
@@ -8,7 +9,7 @@ from typing import Optional
 from typing import Callable
 
 import scipy.stats
-from gn3.computations.biweight import calculate_biweight_corr
+import pingouin as pg
 
 
 def map_shared_keys_to_values(target_sample_keys: List,
@@ -49,13 +50,9 @@ def normalize_values(a_values: List,
     ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
 
     """
-    a_new = []
-    b_new = []
     for a_val, b_val in zip(a_values, b_values):
         if (a_val and b_val is not None):
-            a_new.append(a_val)
-            b_new.append(b_val)
-    return a_new, b_new, len(a_new)
+            yield a_val, b_val
 
 
 def compute_corr_coeff_p_value(primary_values: List, target_values: List,
@@ -81,8 +78,10 @@ def compute_sample_r_correlation(trait_name, corr_method, trait_vals,
     correlation coeff and p value
 
     """
-    (sanitized_traits_vals, sanitized_target_vals,
-     num_overlap) = normalize_values(trait_vals, target_samples_vals)
+
+    sanitized_traits_vals, sanitized_target_vals = list(
+        zip(*list(normalize_values(trait_vals, target_samples_vals))))
+    num_overlap = len(sanitized_traits_vals)
 
     if num_overlap > 5:
 
@@ -102,11 +101,10 @@ package :not packaged in guix
 
     """
 
-    try:
-        results = calculate_biweight_corr(x_val, y_val)
-        return results
-    except Exception as error:
-        raise error
+    results = pg.corr(x_val, y_val, method="bicor")
+    corr_coeff = results["r"].values[0]
+    p_val = results["p-val"].values[0]
+    return (corr_coeff, p_val)
 
 
 def filter_shared_sample_keys(this_samplelist,
@@ -115,13 +113,9 @@ def filter_shared_sample_keys(this_samplelist,
     filter the values using the shared keys
 
     """
-    this_vals = []
-    target_vals = []
     for key, value in target_samplelist.items():
         if key in this_samplelist:
-            target_vals.append(value)
-            this_vals.append(this_samplelist[key])
-    return (this_vals, target_vals)
+            yield this_samplelist[key], value
 
 
 def fast_compute_all_sample_correlation(this_trait,
@@ -140,9 +134,10 @@ def fast_compute_all_sample_correlation(this_trait,
     for target_trait in target_dataset:
         trait_name = target_trait.get("trait_id")
         target_trait_data = target_trait["trait_sample_data"]
-        processed_values.append((trait_name, corr_method, *filter_shared_sample_keys(
-            this_trait_samples, target_trait_data)))
-    with multiprocessing.Pool(4) as pool:
+        processed_values.append((trait_name, corr_method,
+                                 list(zip(*list(filter_shared_sample_keys(
+                                     this_trait_samples, target_trait_data))))))
+    with closing(multiprocessing.Pool()) as pool:
         results = pool.starmap(compute_sample_r_correlation, processed_values)
 
         for sample_correlation in results:
@@ -173,8 +168,8 @@ def compute_all_sample_correlation(this_trait,
     for target_trait in target_dataset:
         trait_name = target_trait.get("trait_id")
         target_trait_data = target_trait["trait_sample_data"]
-        this_vals, target_vals = filter_shared_sample_keys(
-            this_trait_samples, target_trait_data)
+        this_vals, target_vals = list(zip(*list(filter_shared_sample_keys(
+            this_trait_samples, target_trait_data))))
 
         sample_correlation = compute_sample_r_correlation(
             trait_name=trait_name,
diff --git a/gn3/computations/correlations2.py b/gn3/computations/correlations2.py
index 93db3fa..d0222ae 100644
--- a/gn3/computations/correlations2.py
+++ b/gn3/computations/correlations2.py
@@ -6,45 +6,21 @@ FUNCTIONS:
 compute_correlation:
     TODO: Describe what the function does..."""
 
-from math import sqrt
-from functools import reduce
+from scipy import stats
 ## From GN1: mostly for clustering and heatmap generation
 
 def __items_with_values(dbdata, userdata):
     """Retains only corresponding items in the data items that are not `None` values.
     This should probably be renamed to something sensible"""
-    def both_not_none(item1, item2):
-        """Check that both items are not the value `None`."""
-        if (item1 is not None) and (item2 is not None):
-            return (item1, item2)
-        return None
-    def split_lists(accumulator, item):
-        """Separate the 'x' and 'y' items."""
-        return [accumulator[0] + [item[0]], accumulator[1] + [item[1]]]
-    return reduce(
-        split_lists,
-        filter(lambda x: x is not None, map(both_not_none, dbdata, userdata)),
-        [[], []])
+    filtered = [x for x in zip(dbdata, userdata) if x[0] is not None and x[1] is not None]
+    return tuple(zip(*filtered)) if filtered else ([], [])
 
 def compute_correlation(dbdata, userdata):
-    """Compute some form of correlation.
+    """Compute the Pearson correlation coefficient.
 
     This is extracted from
     https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/webqtlUtil.py#L622-L647
     """
     x_items, y_items = __items_with_values(dbdata, userdata)
-    if len(x_items) < 6:
-        return (0.0, len(x_items))
-    meanx = sum(x_items)/len(x_items)
-    meany = sum(y_items)/len(y_items)
-    def cal_corr_vals(acc, item):
-        xitem, yitem = item
-        return [
-            acc[0] + ((xitem - meanx) * (yitem - meany)),
-            acc[1] + ((xitem - meanx) * (xitem - meanx)),
-            acc[2] + ((yitem - meany) * (yitem - meany))]
-    xyd, sxd, syd = reduce(cal_corr_vals, zip(x_items, y_items), [0.0, 0.0, 0.0])
-    try:
-        return ((xyd/(sqrt(sxd)*sqrt(syd))), len(x_items))
-    except ZeroDivisionError:
-        return(0, len(x_items))
+    correlation = stats.pearsonr(x_items, y_items)[0] if len(x_items) >= 6 else 0
+    return (correlation, len(x_items))
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
new file mode 100644
index 0000000..231b0a7
--- /dev/null
+++ b/gn3/computations/partial_correlations.py
@@ -0,0 +1,696 @@
+"""
+This module deals with partial correlations.
+
+It is an attempt to migrate over the partial correlations feature from
+GeneNetwork1.
+"""
+
+import math
+from functools import reduce, partial
+from typing import Any, Tuple, Union, Sequence
+
+import pandas
+import pingouin
+from scipy.stats import pearsonr, spearmanr
+
+from gn3.settings import TEXTDIR
+from gn3.random import random_string
+from gn3.function_helpers import  compose
+from gn3.data_helpers import parse_csv_line
+from gn3.db.traits import export_informative
+from gn3.db.traits import retrieve_trait_info, retrieve_trait_data
+from gn3.db.species import species_name, translate_to_mouse_gene_id
+from gn3.db.correlations import (
+    get_filename,
+    fetch_all_database_data,
+    check_for_literature_info,
+    fetch_tissue_correlations,
+    fetch_literature_correlations,
+    check_symbol_for_tissue_correlation,
+    fetch_gene_symbol_tissue_value_dict_for_trait)
+
+def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]):
+    """
+    Fetches data for the control traits.
+
+    This migrates `web/webqtl/correlation/correlationFunction.controlStrain` in
+    GN1, with a few modifications to the arguments passed in.
+
+    PARAMETERS:
+    controls: A map of sample names to trait data. Equivalent to the `cvals`
+        value in the corresponding source function in GN1.
+    sampleslist: A list of samples. Equivalent to `strainlst` in the
+        corresponding source function in GN1
+    """
+    def __process_control__(trait_data):
+        def __process_sample__(acc, sample):
+            if sample in trait_data["data"].keys():
+                sample_item = trait_data["data"][sample]
+                val = sample_item["value"]
+                if val is not None:
+                    return (
+                        acc[0] + (sample,),
+                        acc[1] + (val,),
+                        acc[2] + (sample_item["variance"],))
+            return acc
+        return reduce(
+            __process_sample__, sampleslist, (tuple(), tuple(), tuple()))
+
+    return reduce(
+        lambda acc, item: (
+            acc[0] + (item[0],),
+            acc[1] + (item[1],),
+            acc[2] + (item[2],),
+            acc[3] + (len(item[0]),),
+        ),
+        [__process_control__(trait_data) for trait_data in controls],
+        (tuple(), tuple(), tuple(), tuple()))
+
+def dictify_by_samples(samples_vals_vars: Sequence[Sequence]) -> Sequence[dict]:
+    """
+    Build a sequence of dictionaries from a sequence of separate sequences of
+    samples, values and variances.
+
+    This is a partial migration of
+    `web.webqtl.correlation.correlationFunction.fixStrains` function in GN1.
+    This implementation extracts code that will find common use, and that will
+    find use in more than one place.
+    """
+    return tuple(
+        {
+            sample: {"sample_name": sample, "value": val, "variance": var}
+            for sample, val, var in zip(*trait_line)
+        } for trait_line in zip(*(samples_vals_vars[0:3])))
+
+def fix_samples(primary_trait: dict, control_traits: Sequence[dict]) -> Sequence[Sequence[Any]]:
+    """
+    Corrects sample_names, values and variance such that they all contain only
+    those samples that are common to the reference trait and all control traits.
+
+    This is a partial migration of the
+    `web.webqtl.correlation.correlationFunction.fixStrain` function in GN1.
+    """
+    primary_samples = tuple(
+        present[0] for present in
+        ((sample, all(sample in control.keys() for control in control_traits))
+         for sample in primary_trait.keys())
+        if present[1])
+    control_vals_vars: tuple = reduce(
+        lambda acc, x: (acc[0] + (x[0],), acc[1] + (x[1],)),
+        ((item["value"], item["variance"])
+         for sublist in [tuple(control.values()) for control in control_traits]
+         for item in sublist),
+        (tuple(), tuple()))
+    return (
+        primary_samples,
+        tuple(primary_trait[sample]["value"] for sample in primary_samples),
+        control_vals_vars[0],
+        tuple(primary_trait[sample]["variance"] for sample in primary_samples),
+        control_vals_vars[1])
+
+def find_identical_traits(
+        primary_name: str, primary_value: float, control_names: Tuple[str, ...],
+        control_values: Tuple[float, ...]) -> Tuple[str, ...]:
+    """
+    Find traits that have the same value when the values are considered to
+    3 decimal places.
+
+    This is a migration of the
+    `web.webqtl.correlation.correlationFunction.findIdenticalTraits` function in
+    GN1.
+    """
+    def __merge_identicals__(
+            acc: Tuple[str, ...],
+            ident: Tuple[str, Tuple[str, ...]]) -> Tuple[str, ...]:
+        return acc + ident[1]
+
+    def __dictify_controls__(acc, control_item):
+        ckey = tuple("{:.3f}".format(item) for item in control_item[0])
+        return {**acc, ckey: acc.get(ckey, tuple()) + (control_item[1],)}
+
+    return (reduce(## for identical control traits
+        __merge_identicals__,
+        (item for item in reduce(# type: ignore[var-annotated]
+            __dictify_controls__, zip(control_values, control_names),
+            {}).items() if len(item[1]) > 1),
+        tuple())
+            or
+            reduce(## If no identical control traits, try primary and controls
+                __merge_identicals__,
+                (item for item in reduce(# type: ignore[var-annotated]
+                    __dictify_controls__,
+                    zip((primary_value,) + control_values,
+                        (primary_name,) + control_names), {}).items()
+                 if len(item[1]) > 1),
+                tuple()))
+
+def tissue_correlation(
+        primary_trait_values: Tuple[float, ...],
+        target_trait_values: Tuple[float, ...],
+        method: str) -> Tuple[float, float]:
+    """
+    Compute the correlation between the primary trait values, and the values of
+    a single target value.
+
+    This migrates the `cal_tissue_corr` function embedded in the larger
+    `web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in
+    GeneNetwork1.
+    """
+    def spearman_corr(*args):
+        result = spearmanr(*args)
+        return (result.correlation, result.pvalue)
+
+    method_fns = {"pearson": pearsonr, "spearman": spearman_corr}
+
+    assert len(primary_trait_values) == len(target_trait_values), (
+        "The lengths of the `primary_trait_values` and `target_trait_values` "
+        "must be equal")
+    assert method in method_fns.keys(), (
+        "Method must be one of: {}".format(",".join(method_fns.keys())))
+
+    corr, pvalue = method_fns[method](primary_trait_values, target_trait_values)
+    return (corr, pvalue)
+
+def batch_computed_tissue_correlation(
+        primary_trait_values: Tuple[float, ...], target_traits_dict: dict,
+        method: str) -> Tuple[dict, dict]:
+    """
+    This is a migration of the
+    `web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in
+    GeneNetwork1
+    """
+    def __corr__(acc, target):
+        corr = tissue_correlation(primary_trait_values, target[1], method)
+        return ({**acc[0], target[0]: corr[0]}, {**acc[0], target[1]: corr[1]})
+    return reduce(__corr__, target_traits_dict.items(), ({}, {}))
+
+def correlations_of_all_tissue_traits(
+        primary_trait_symbol_value_dict: dict, symbol_value_dict: dict,
+        method: str) -> Tuple[dict, dict]:
+    """
+    Computes and returns the correlation of all tissue traits.
+
+    This is a migration of the
+    `web.webqtl.correlation.correlationFunction.calculateCorrOfAllTissueTrait`
+    function in GeneNetwork1.
+    """
+    primary_trait_values = tuple(primary_trait_symbol_value_dict.values())[0]
+    return batch_computed_tissue_correlation(
+        primary_trait_values, symbol_value_dict, method)
+
+def good_dataset_samples_indexes(
+        samples: Tuple[str, ...],
+        samples_from_file: Tuple[str, ...]) -> Tuple[int, ...]:
+    """
+    Return the indexes of the items in `samples_from_files` that are also found
+    in `samples`.
+
+    This is a partial migration of the
+    `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
+    function in GeneNetwork1.
+    """
+    return tuple(sorted(
+        samples_from_file.index(good) for good in
+        set(samples).intersection(set(samples_from_file))))
+
+def partial_correlations_fast(# pylint: disable=[R0913, R0914]
+        samples, primary_vals, control_vals, database_filename,
+        fetched_correlations, method: str, correlation_type: str) -> Tuple[
+            float, Tuple[float, ...]]:
+    """
+    Computes partial correlation coefficients using data from a CSV file.
+
+    This is a partial migration of the
+    `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
+    function in GeneNetwork1.
+    """
+    assert method in ("spearman", "pearson")
+    with open(database_filename, "r") as dataset_file:
+        dataset = tuple(dataset_file.readlines())
+
+    good_dataset_samples = good_dataset_samples_indexes(
+        samples, parse_csv_line(dataset[0])[1:])
+
+    def __process_trait_names_and_values__(acc, line):
+        trait_line = parse_csv_line(line)
+        trait_name = trait_line[0]
+        trait_data = trait_line[1:]
+        if trait_name in fetched_correlations.keys():
+            return (
+                acc[0] + (trait_name,),
+                acc[1] + tuple(
+                    trait_data[i] if i in good_dataset_samples else None
+                    for i in range(len(trait_data))))
+        return acc
+
+    processed_trait_names_values: tuple = reduce(
+        __process_trait_names_and_values__, dataset[1:], (tuple(), tuple()))
+    all_target_trait_names: Tuple[str, ...] = processed_trait_names_values[0]
+    all_target_trait_values: Tuple[float, ...] = processed_trait_names_values[1]
+
+    all_correlations = compute_partial(
+        primary_vals, control_vals, all_target_trait_names,
+        all_target_trait_values, method)
+    ## Line 772 to 779 in GN1 are the cause of the weird complexity in the
+    ## return below. Once the surrounding code is successfully migrated and
+    ## reworked, this complexity might go away, by getting rid of the
+    ## `correlation_type` parameter
+    return len(all_correlations), tuple(
+        corr + (
+            (fetched_correlations[corr[0]],) if correlation_type == "literature"
+            else fetched_correlations[corr[0]][0:2])
+        for idx, corr in enumerate(all_correlations))
+
+def build_data_frame(
+        xdata: Tuple[float, ...], ydata: Tuple[float, ...],
+        zdata: Union[
+            Tuple[float, ...],
+            Tuple[Tuple[float, ...], ...]]) -> pandas.DataFrame:
+    """
+    Build a pandas DataFrame object from xdata, ydata and zdata
+    """
+    x_y_df = pandas.DataFrame({"x": xdata, "y": ydata})
+    if isinstance(zdata[0], float):
+        return x_y_df.join(pandas.DataFrame({"z": zdata}))
+    interm_df = x_y_df.join(pandas.DataFrame(
+        {"z{}".format(i): val for i, val in enumerate(zdata)}))
+    if interm_df.shape[1] == 3:
+        return interm_df.rename(columns={"z0": "z"})
+    return interm_df
+
+def compute_partial(
+        primary_vals, control_vals, target_vals, target_names,
+        method: str) -> Tuple[
+            Union[
+                Tuple[str, int, float, float, float, float], None],
+            ...]:
+    """
+    Compute the partial correlations.
+
+    This is a re-implementation of the
+    `web.webqtl.correlation.correlationFunction.determinePartialsByR` function
+    in GeneNetwork1.
+
+    This implementation reworks the child function `compute_partial` which will
+    then be used in the place of `determinPartialsByR`.
+
+    TODO: moving forward, we might need to use the multiprocessing library to
+    speed up the computations, in case they are found to be slow.
+    """
+    # replace the R code with `pingouin.partial_corr`
+    def __compute_trait_info__(target):
+        targ_vals = target[0]
+        targ_name = target[1]
+        primary = [
+            prim for targ, prim in zip(targ_vals, primary_vals)
+            if targ is not None]
+
+        datafrm = build_data_frame(
+            primary,
+            tuple(targ for targ in targ_vals if targ is not None),
+            tuple(cont for i, cont in enumerate(control_vals)
+                  if target[i] is not None))
+        covariates = "z" if datafrm.shape[1] == 3 else [
+            col for col in datafrm.columns if col not in ("x", "y")]
+        ppc = pingouin.partial_corr(
+            data=datafrm, x="x", y="y", covar=covariates, method=(
+                "pearson" if "pearson" in method.lower() else "spearman"))
+        pc_coeff = ppc["r"][0]
+
+        zero_order_corr = pingouin.corr(
+            datafrm["x"], datafrm["y"], method=(
+                "pearson" if "pearson" in method.lower() else "spearman"))
+
+        if math.isnan(pc_coeff):
+            return (
+                targ_name, len(primary), pc_coeff, 1, zero_order_corr["r"][0],
+                zero_order_corr["p-val"][0])
+        return (
+            targ_name, len(primary), pc_coeff,
+            (ppc["p-val"][0] if not math.isnan(ppc["p-val"][0]) else (
+                0 if (abs(pc_coeff - 1) < 0.0000001) else 1)),
+            zero_order_corr["r"][0], zero_order_corr["p-val"][0])
+
+    return tuple(
+        __compute_trait_info__(target)
+        for target in zip(target_vals, target_names))
+
+def partial_correlations_normal(# pylint: disable=R0913
+        primary_vals, control_vals, input_trait_gene_id, trait_database,
+        data_start_pos: int, db_type: str, method: str) -> Tuple[
+            float, Tuple[float, ...]]:
+    """
+    Computes the correlation coefficients.
+
+    This is a migration of the
+    `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsNormal`
+    function in GeneNetwork1.
+    """
+    def __add_lit_and_tiss_corr__(item):
+        if method.lower() == "sgo literature correlation":
+            # if method is 'SGO Literature Correlation', `compute_partial`
+            # would give us LitCorr in the [1] position
+            return tuple(item) + trait_database[1]
+        if method.lower() in (
+                "tissue correlation, pearson's r",
+                "tissue correlation, spearman's rho"):
+            # if method is 'Tissue Correlation, *', `compute_partial` would give
+            # us Tissue Corr in the [1] position and Tissue Corr P Value in the
+            # [2] position
+            return tuple(item) + (trait_database[1], trait_database[2])
+        return item
+
+    target_trait_names, target_trait_vals = reduce(
+        lambda acc, item: (acc[0]+(item[0],), acc[1]+(item[data_start_pos:],)),
+        trait_database, (tuple(), tuple()))
+
+    all_correlations = compute_partial(
+        primary_vals, control_vals, target_trait_vals, target_trait_names,
+        method)
+
+    if (input_trait_gene_id and db_type == "ProbeSet" and method.lower() in (
+            "sgo literature correlation", "tissue correlation, pearson's r",
+            "tissue correlation, spearman's rho")):
+        return (
+            len(trait_database),
+            tuple(
+                __add_lit_and_tiss_corr__(item)
+                for idx, item in enumerate(all_correlations)))
+
+    return len(trait_database), all_correlations
+
+def partial_corrs(# pylint: disable=[R0913]
+        conn, samples, primary_vals, control_vals, return_number, species,
+        input_trait_geneid, input_trait_symbol, tissue_probeset_freeze_id,
+        method, dataset, database_filename):
+    """
+    Compute the partial correlations, selecting the fast or normal method
+    depending on the existence of the database text file.
+
+    This is a partial migration of the
+    `web.webqtl.correlation.PartialCorrDBPage.__init__` function in
+    GeneNetwork1.
+    """
+    if database_filename:
+        return partial_correlations_fast(
+            samples, primary_vals, control_vals, database_filename,
+            (
+                fetch_literature_correlations(
+                    species, input_trait_geneid, dataset, return_number, conn)
+                if "literature" in method.lower() else
+                fetch_tissue_correlations(
+                    dataset, input_trait_symbol, tissue_probeset_freeze_id,
+                    method, return_number, conn)),
+            method,
+            ("literature" if method.lower() == "sgo literature correlation"
+             else ("tissue" if "tissue" in method.lower() else "genetic")))
+
+    trait_database, data_start_pos = fetch_all_database_data(
+        conn, species, input_trait_geneid, input_trait_symbol, samples, dataset,
+        method, return_number, tissue_probeset_freeze_id)
+    return partial_correlations_normal(
+        primary_vals, control_vals, input_trait_geneid, trait_database,
+        data_start_pos, dataset, method)
+
+def literature_correlation_by_list(
+        conn: Any, species: str, trait_list: Tuple[dict]) -> Tuple[dict]:
+    """
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.getLiteratureCorrelationByList`
+    function in GeneNetwork1.
+    """
+    if any((lambda t: (
+            bool(t.get("tissue_corr")) and
+            bool(t.get("tissue_p_value"))))(trait)
+           for trait in trait_list):
+        temporary_table_name = f"LITERATURE{random_string(8)}"
+        query1 = (
+            f"CREATE TEMPORARY TABLE {temporary_table_name} "
+            "(GeneId1 INT(12) UNSIGNED, GeneId2 INT(12) UNSIGNED PRIMARY KEY, "
+            "value DOUBLE)")
+        query2 = (
+            f"INSERT INTO {temporary_table_name}(GeneId1, GeneId2, value) "
+            "SELECT GeneId1, GeneId2, value FROM LCorrRamin3 "
+            "WHERE GeneId1=%(geneid)s")
+        query3 = (
+            "INSERT INTO {temporary_table_name}(GeneId1, GeneId2, value) "
+            "SELECT GeneId2, GeneId1, value FROM LCorrRamin3 "
+            "WHERE GeneId2=%s AND GeneId1 != %(geneid)s")
+
+        def __set_mouse_geneid__(trait):
+            if trait.get("geneid"):
+                return {
+                    **trait,
+                    "mouse_geneid": translate_to_mouse_gene_id(
+                        species, trait.get("geneid"), conn)
+                }
+            return {**trait, "mouse_geneid": 0}
+
+        def __retrieve_lcorr__(cursor, geneids):
+            cursor.execute(
+                f"SELECT GeneId2, value FROM {temporary_table_name} "
+                "WHERE GeneId2 IN %(geneids)s",
+                geneids=geneids)
+            return dict(cursor.fetchall())
+
+        with conn.cursor() as cursor:
+            cursor.execute(query1)
+            cursor.execute(query2)
+            cursor.execute(query3)
+
+            traits = tuple(__set_mouse_geneid__(trait) for trait in trait_list)
+            lcorrs = __retrieve_lcorr__(
+                cursor, (
+                    trait["mouse_geneid"] for trait in traits
+                    if (trait["mouse_geneid"] != 0 and
+                        trait["mouse_geneid"].find(";") < 0)))
+            return tuple(
+                {**trait, "l_corr": lcorrs.get(trait["mouse_geneid"], None)}
+                for trait in traits)
+
+        return trait_list
+    return trait_list
+
+def tissue_correlation_by_list(
+        conn: Any, primary_trait_symbol: str, tissue_probeset_freeze_id: int,
+        method: str, trait_list: Tuple[dict]) -> Tuple[dict]:
+    """
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.getTissueCorrelationByList`
+    function in GeneNetwork1.
+    """
+    def __add_tissue_corr__(trait, primary_trait_values, trait_values):
+        result = pingouin.corr(
+            primary_trait_values, trait_values,
+            method=("spearman" if "spearman" in method.lower() else "pearson"))
+        return {
+            **trait,
+            "tissue_corr": result["r"],
+            "tissue_p_value": result["p-val"]
+        }
+
+    if any((lambda t: bool(t.get("l_corr")))(trait) for trait in trait_list):
+        prim_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
+            (primary_trait_symbol,), tissue_probeset_freeze_id, conn)
+        if primary_trait_symbol.lower() in prim_trait_symbol_value_dict:
+            primary_trait_value = prim_trait_symbol_value_dict[
+                primary_trait_symbol.lower()]
+            gene_symbol_list = tuple(
+                trait for trait in trait_list if "symbol" in trait.keys())
+            symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
+                gene_symbol_list, tissue_probeset_freeze_id, conn)
+            return tuple(
+                __add_tissue_corr__(
+                    trait, primary_trait_value,
+                    symbol_value_dict[trait["symbol"].lower()])
+                for trait in trait_list
+                if ("symbol" in trait and
+                    bool(trait["symbol"]) and
+                    trait["symbol"].lower() in symbol_value_dict))
+        return tuple({
+            **trait,
+            "tissue_corr": None,
+            "tissue_p_value": None
+        } for trait in trait_list)
+    return trait_list
+
+def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911]
+        conn: Any, primary_trait_name: str,
+        control_trait_names: Tuple[str, ...], method: str,
+        criteria: int, group: str, target_db_name: str) -> dict:
+    """
+    This is the 'ochestration' function for the partial-correlation feature.
+
+    This function will dispatch the functions doing data fetches from the
+    database (and various other places) and feed that data to the functions
+    doing the conversions and computations. It will then return the results of
+    all of that work.
+
+    This function is doing way too much. Look into splitting out the
+    functionality into smaller functions that do fewer things.
+    """
+    threshold = 0
+    corr_min_informative = 4
+
+    primary_trait = retrieve_trait_info(threshold, primary_trait_name, conn)
+    primary_trait_data = retrieve_trait_data(primary_trait, conn)
+    primary_samples, primary_values, _primary_variances = export_informative(
+        primary_trait_data)
+
+    cntrl_traits = tuple(
+        retrieve_trait_info(threshold, trait_full_name, conn)
+        for trait_full_name in control_trait_names)
+    cntrl_traits_data = tuple(
+        retrieve_trait_data(cntrl_trait, conn)
+        for cntrl_trait in cntrl_traits)
+    species = species_name(conn, group)
+
+    (cntrl_samples,
+     cntrl_values,
+     _cntrl_variances,
+     _cntrl_ns) = control_samples(cntrl_traits_data, primary_samples)
+
+    common_primary_control_samples = primary_samples
+    fixed_primary_vals = primary_values
+    fixed_control_vals = cntrl_values
+    if not all(cnt_smp == primary_samples for cnt_smp in cntrl_samples):
+        (common_primary_control_samples,
+         fixed_primary_vals,
+         fixed_control_vals,
+         _primary_variances,
+         _cntrl_variances) = fix_samples(primary_trait, cntrl_traits)
+
+    if len(common_primary_control_samples) < corr_min_informative:
+        return {
+            "status": "error",
+            "message": (
+                f"Fewer than {corr_min_informative} samples data entered for "
+                f"{group} dataset. No calculation of correlation has been "
+                "attempted."),
+            "error_type": "Inadequate Samples"}
+
+    identical_traits_names = find_identical_traits(
+        primary_trait_name, primary_values, control_trait_names, cntrl_values)
+    if len(identical_traits_names) > 0:
+        return {
+            "status": "error",
+            "message": (
+                f"{identical_traits_names[0]} and {identical_traits_names[1]} "
+                "have the same values for the {len(fixed_primary_vals)} "
+                "samples that will be used to compute the partial correlation "
+                "(common for all primary and control traits). In such cases, "
+                "partial correlation cannot be computed. Please re-select your "
+                "traits."),
+            "error_type": "Identical Traits"}
+
+    input_trait_geneid = primary_trait.get("geneid")
+    input_trait_symbol = primary_trait.get("symbol")
+    input_trait_mouse_geneid = translate_to_mouse_gene_id(
+        species, input_trait_geneid, conn)
+
+    tissue_probeset_freeze_id = 1
+    db_type = primary_trait["db"]["dataset_type"]
+
+    if db_type == "ProbeSet" and method.lower() in (
+            "sgo literature correlation",
+            "tissue correlation, pearson's r",
+            "tissue correlation, spearman's rho"):
+        return {
+            "status": "error",
+            "message": (
+                "Wrong correlation type: It is not possible to compute the "
+                f"{method} between your trait and data in the {target_db_name} "
+                "database. Please try again after selecting another type of "
+                "correlation."),
+            "error_type": "Correlation Type"}
+
+    if (method.lower() == "sgo literature correlation" and (
+            input_trait_geneid is None or
+            check_for_literature_info(conn, input_trait_mouse_geneid))):
+        return {
+            "status": "error",
+            "message": (
+                "No Literature Information: This gene does not have any "
+                "associated Literature Information."),
+            "error_type": "Literature Correlation"}
+
+    if (
+            method.lower() in (
+                "tissue correlation, pearson's r",
+                "tissue correlation, spearman's rho")
+            and input_trait_symbol is None):
+        return {
+            "status": "error",
+            "message": (
+                "No Tissue Correlation Information: This gene does not have "
+                "any associated Tissue Correlation Information."),
+            "error_type": "Tissue Correlation"}
+
+    if (
+            method.lower() in (
+                "tissue correlation, pearson's r",
+                "tissue correlation, spearman's rho")
+            and check_symbol_for_tissue_correlation(
+                conn, tissue_probeset_freeze_id, input_trait_symbol)):
+        return {
+            "status": "error",
+            "message": (
+                "No Tissue Correlation Information: This gene does not have "
+                "any associated Tissue Correlation Information."),
+            "error_type": "Tissue Correlation"}
+
+    database_filename = get_filename(conn, target_db_name, TEXTDIR)
+    _total_traits, all_correlations = partial_corrs(
+        conn, common_primary_control_samples, fixed_primary_vals,
+        fixed_control_vals, len(fixed_primary_vals), species,
+        input_trait_geneid, input_trait_symbol, tissue_probeset_freeze_id,
+        method, primary_trait["db"], database_filename)
+
+
+    def __make_sorter__(method):
+        def __sort_6__(row):
+            return row[6]
+
+        def __sort_3__(row):
+            return row[3]
+
+        if "literature" in method.lower():
+            return __sort_6__
+
+        if "tissue" in method.lower():
+            return __sort_6__
+
+        return __sort_3__
+
+    sorted_correlations = sorted(
+        all_correlations, key=__make_sorter__(method))
+
+    add_lit_corr_and_tiss_corr = compose(
+        partial(literature_correlation_by_list, conn, species),
+        partial(
+            tissue_correlation_by_list, conn, input_trait_symbol,
+            tissue_probeset_freeze_id, method))
+
+    trait_list = add_lit_corr_and_tiss_corr(tuple(
+        {
+            **retrieve_trait_info(
+                threshold,
+                f"{primary_trait['db']['dataset_name']}::{item[0]}",
+                conn),
+            "noverlap": item[1],
+            "partial_corr": item[2],
+            "partial_corr_p_value": item[3],
+            "corr": item[4],
+            "corr_p_value": item[5],
+            "rank_order": (1 if "spearman" in method.lower() else 0),
+            **({
+                "tissue_corr": item[6],
+                "tissue_p_value": item[7]}
+               if len(item) == 8 else {}),
+            **({"l_corr": item[6]}
+               if len(item) == 7 else {})
+        }
+        for item in
+        sorted_correlations[:min(criteria, len(all_correlations))]))
+
+    return trait_list
diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py
index fd508fa..ab12fe7 100644
--- a/gn3/computations/wgcna.py
+++ b/gn3/computations/wgcna.py
@@ -3,8 +3,11 @@
 import os
 import json
 import uuid
-from gn3.settings import TMPDIR
+import subprocess
+import base64
+
 
+from gn3.settings import TMPDIR
 from gn3.commands import run_cmd
 
 
@@ -14,12 +17,46 @@ def dump_wgcna_data(request_data: dict):
 
     temp_file_path = os.path.join(TMPDIR, filename)
 
+    request_data["TMPDIR"] = TMPDIR
+
     with open(temp_file_path, "w") as output_file:
         json.dump(request_data, output_file)
 
     return temp_file_path
 
 
+def stream_cmd_output(socketio, request_data, cmd: str):
+    """function to stream in realtime"""
+    # xtodo  syncing and closing /edge cases
+
+    socketio.emit("output", {"data": f"calling you script {cmd}"},
+                  namespace="/", room=request_data["socket_id"])
+    results = subprocess.Popen(
+        cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
+
+    if results.stdout is not None:
+
+        for line in iter(results.stdout.readline, b""):
+            socketio.emit("output",
+                          {"data": line.decode("utf-8").rstrip()},
+                          namespace="/", room=request_data["socket_id"])
+
+        socketio.emit(
+            "output", {"data":
+                       "parsing the output results"}, namespace="/",
+            room=request_data["socket_id"])
+
+
+def process_image(image_loc: str) -> bytes:
+    """encode the image"""
+
+    try:
+        with open(image_loc, "rb") as image_file:
+            return base64.b64encode(image_file.read())
+    except FileNotFoundError:
+        return b""
+
+
 def compose_wgcna_cmd(rscript_path: str, temp_file_path: str):
     """function to componse wgcna cmd"""
     # (todo):issue relative paths to abs paths
@@ -32,6 +69,8 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
     generated_file = dump_wgcna_data(request_data)
     cmd = compose_wgcna_cmd(rscript_path, generated_file)
 
+    # stream_cmd_output(request_data, cmd)  disable streaming of data
+
     try:
 
         run_cmd_results = run_cmd(cmd)
@@ -40,8 +79,14 @@ def call_wgcna_script(rscript_path: str, request_data: dict):
 
             if run_cmd_results["code"] != 0:
                 return run_cmd_results
+
+            output_file_data = json.load(outputfile)
+            output_file_data["output"]["image_data"] = process_image(
+                output_file_data["output"]["imageLoc"]).decode("ascii")
+            # json format only supports  unicode string// to get image data reconvert
+
             return {
-                "data": json.load(outputfile),
+                "data": output_file_data,
                 **run_cmd_results
             }
     except FileNotFoundError:
diff --git a/gn3/data_helpers.py b/gn3/data_helpers.py
new file mode 100644
index 0000000..b72fbc5
--- /dev/null
+++ b/gn3/data_helpers.py
@@ -0,0 +1,52 @@
+"""
+This module will hold generic functions that can operate on a wide-array of
+data structures.
+"""
+
+from math import ceil
+from functools import reduce
+from typing import Any, Tuple, Sequence, Optional
+
+def partition_all(num: int, items: Sequence[Any]) -> Tuple[Tuple[Any, ...], ...]:
+    """
+    Given a sequence `items`, return a new sequence of the same type as `items`
+    with the data partitioned into sections of `n` items per partition.
+
+    This is an approximation of clojure's `partition-all` function.
+    """
+    def __compute_start_stop__(acc, iteration):
+        start = iteration * num
+        return acc + ((start, start + num),)
+
+    iterations = range(ceil(len(items) / num))
+    return tuple([# type: ignore[misc]
+        tuple(items[start:stop]) for start, stop # type: ignore[has-type]
+        in reduce(
+            __compute_start_stop__, iterations, tuple())])
+
+def partition_by(partition_fn, items):
+    """
+    Given a sequence `items`, return a tuple of tuples, each of which contain
+    the values in `items` partitioned such that the first item in each internal
+    tuple, when passed to `partition_function` returns True.
+
+    This is an approximation of Clojure's `partition-by` function.
+    """
+    def __partitioner__(accumulator, item):
+        if partition_fn(item):
+            return accumulator + ((item,),)
+        return accumulator[:-1] + (accumulator[-1] + (item,),)
+
+    return reduce(__partitioner__, items, tuple())
+
+def parse_csv_line(
+        line: str, delimiter: str = ",",
+        quoting: Optional[str] = '"') -> Tuple[str, ...]:
+    """
+    Parses a line from a CSV file into a tuple of strings.
+
+    This is a migration of the `web.webqtl.utility.webqtlUtil.readLineCSV`
+    function in GeneNetwork1.
+    """
+    return tuple(
+        col.strip("{} \t\n".format(quoting)) for col in line.split(delimiter))
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
new file mode 100644
index 0000000..3d12019
--- /dev/null
+++ b/gn3/db/correlations.py
@@ -0,0 +1,564 @@
+"""
+This module will hold functions that are used in the (partial) correlations
+feature to access the database to retrieve data needed for computations.
+"""
+import os
+from functools import reduce
+from typing import Any, Dict, Tuple, Union
+
+from gn3.random import random_string
+from gn3.data_helpers import partition_all
+from gn3.db.species import translate_to_mouse_gene_id
+
+def get_filename(conn: Any, target_db_name: str, text_files_dir: str) -> Union[
+        str, bool]:
+    """
+    Retrieve the name of the reference database file with which correlations are
+    computed.
+
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.getFileName` function in
+    GeneNetwork1.
+    """
+    with conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT Id, FullName from ProbeSetFreeze WHERE Name=%s",
+            (target_db_name,))
+        result = cursor.fetchone()
+        if result:
+            filename = "ProbeSetFreezeId_{tid}_FullName_{fname}.txt".format(
+                tid=result[0],
+                fname=result[1].replace(' ', '_').replace('/', '_'))
+            return ((filename in os.listdir(text_files_dir))
+                    and f"{text_files_dir}/{filename}")
+
+    return False
+
+def build_temporary_literature_table(
+        conn: Any, species: str, gene_id: int, return_number: int) -> str:
+    """
+    Build and populate a temporary table to hold the literature correlation data
+    to be used in computations.
+
+    "This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.getTempLiteratureTable` function in
+    GeneNetwork1.
+    """
+    def __translated_species_id(row, cursor):
+        if species == "mouse":
+            return row[1]
+        query = {
+            "rat": "SELECT rat FROM GeneIDXRef WHERE mouse=%s",
+            "human": "SELECT human FROM GeneIDXRef WHERE mouse=%d"}
+        if species in query.keys():
+            cursor.execute(query[species], row[1])
+            record = cursor.fetchone()
+            if record:
+                return record[0]
+            return None
+        return None
+
+    temp_table_name = f"TOPLITERATURE{random_string(8)}"
+    with conn.cursor as cursor:
+        mouse_geneid = translate_to_mouse_gene_id(species, gene_id, conn)
+        data_query = (
+            "SELECT GeneId1, GeneId2, value FROM LCorrRamin3 "
+            "WHERE GeneId1 = %(mouse_gene_id)s "
+            "UNION ALL "
+            "SELECT GeneId2, GeneId1, value FROM LCorrRamin3 "
+            "WHERE GeneId2 = %(mouse_gene_id)s "
+            "AND GeneId1 != %(mouse_gene_id)s")
+        cursor.execute(
+            (f"CREATE TEMPORARY TABLE {temp_table_name} ("
+             "GeneId1 int(12) unsigned, "
+             "GeneId2 int(12) unsigned PRIMARY KEY, "
+             "value double)"))
+        cursor.execute(data_query, mouse_gene_id=mouse_geneid)
+        literature_data = [
+            {"GeneId1": row[0], "GeneId2": row[1], "value": row[2]}
+            for row in cursor.fetchall()
+            if __translated_species_id(row, cursor)]
+
+        cursor.execute(
+            (f"INSERT INTO {temp_table_name} "
+             "VALUES (%(GeneId1)s, %(GeneId2)s, %(value)s)"),
+            literature_data[0:(2 * return_number)])
+
+    return temp_table_name
+
+def fetch_geno_literature_correlations(temp_table: str) -> str:
+    """
+    Helper function for `fetch_literature_correlations` below, to build query
+    for `Geno*` tables.
+    """
+    return (
+        f"SELECT Geno.Name, {temp_table}.value "
+        "FROM Geno, GenoXRef, GenoFreeze "
+        f"LEFT JOIN {temp_table} ON {temp_table}.GeneId2=ProbeSet.GeneId "
+        "WHERE ProbeSet.GeneId IS NOT NULL "
+        f"AND {temp_table}.value IS NOT NULL "
+        "AND GenoXRef.GenoFreezeId = GenoFreeze.Id "
+        "AND GenoFreeze.Name = %(db_name)s "
+        "AND Geno.Id=GenoXRef.GenoId "
+        "ORDER BY Geno.Id")
+
+def fetch_probeset_literature_correlations(temp_table: str) -> str:
+    """
+    Helper function for `fetch_literature_correlations` below, to build query
+    for `ProbeSet*` tables.
+    """
+    return (
+        f"SELECT ProbeSet.Name, {temp_table}.value "
+        "FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze "
+        "LEFT JOIN {temp_table} ON {temp_table}.GeneId2=ProbeSet.GeneId "
+        "WHERE ProbeSet.GeneId IS NOT NULL "
+        "AND {temp_table}.value IS NOT NULL "
+        "AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
+        "AND ProbeSetFreeze.Name = %(db_name)s "
+        "AND ProbeSet.Id=ProbeSetXRef.ProbeSetId "
+        "ORDER BY ProbeSet.Id")
+
+def fetch_literature_correlations(
+        species: str, gene_id: int, dataset: dict, return_number: int,
+        conn: Any) -> dict:
+    """
+    Gather the literature correlation data and pair it with trait id string(s).
+
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.fetchLitCorrelations` function in
+    GeneNetwork1.
+    """
+    temp_table = build_temporary_literature_table(
+        conn, species, gene_id, return_number)
+    query_fns = {
+        "Geno": fetch_geno_literature_correlations,
+        # "Temp": fetch_temp_literature_correlations,
+        # "Publish": fetch_publish_literature_correlations,
+        "ProbeSet": fetch_probeset_literature_correlations}
+    with conn.cursor as cursor:
+        cursor.execute(
+            query_fns[dataset["dataset_type"]](temp_table),
+            db_name=dataset["dataset_name"])
+        results = cursor.fetchall()
+        cursor.execute("DROP TEMPORARY TABLE %s", temp_table)
+        return dict(results)
+
+def fetch_symbol_value_pair_dict(
+        symbol_list: Tuple[str, ...], data_id_dict: dict,
+        conn: Any) -> Dict[str, Tuple[float, ...]]:
+    """
+    Map each gene symbols to the corresponding tissue expression data.
+
+    This is a migration of the
+    `web.webqtl.correlation.correlationFunction.getSymbolValuePairDict` function
+    in GeneNetwork1.
+    """
+    data_ids = {
+        symbol: data_id_dict.get(symbol) for symbol in symbol_list
+        if data_id_dict.get(symbol) is not None
+    }
+    query = "SELECT Id, value FROM TissueProbeSetData WHERE Id IN %(data_ids)s"
+    with conn.cursor() as cursor:
+        cursor.execute(
+            query,
+            data_ids=tuple(data_ids.values()))
+        value_results = cursor.fetchall()
+        return {
+            key: tuple(row[1] for row in value_results if row[0] == key)
+            for key in data_ids.keys()
+        }
+
+    return {}
+
+def fetch_gene_symbol_tissue_value_dict(
+        symbol_list: Tuple[str, ...], data_id_dict: dict, conn: Any,
+        limit_num: int = 1000) -> dict:#getGeneSymbolTissueValueDict
+    """
+    Wrapper function for `gn3.db.correlations.fetch_symbol_value_pair_dict`.
+
+    This is a migrations of the
+    `web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDict` in
+    GeneNetwork1.
+    """
+    count = len(symbol_list)
+    if count != 0 and count <= limit_num:
+        return fetch_symbol_value_pair_dict(symbol_list, data_id_dict, conn)
+
+    if count > limit_num:
+        return {
+            key: value for dct in [
+                fetch_symbol_value_pair_dict(sl, data_id_dict, conn)
+                for sl in partition_all(limit_num, symbol_list)]
+            for key, value in dct.items()
+        }
+
+    return {}
+
+def fetch_tissue_probeset_xref_info(
+        gene_name_list: Tuple[str, ...], probeset_freeze_id: int,
+        conn: Any) -> Tuple[tuple, dict, dict, dict, dict, dict, dict]:
+    """
+    Retrieve the ProbeSet XRef information for tissues.
+
+    This is a migration of the
+    `web.webqtl.correlation.correlationFunction.getTissueProbeSetXRefInfo`
+    function in GeneNetwork1."""
+    with conn.cursor() as cursor:
+        if len(gene_name_list) == 0:
+            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=%(probeset_freeze_id)s "
+                "  AND 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")
+            cursor.execute(query, probeset_freeze_id=probeset_freeze_id)
+        else:
+            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=%(probeset_freeze_id)s "
+                "  AND Symbol in %(symbols)s "
+                "  GROUP BY Symbol"
+                ") AS x "
+                "INNER JOIN TissueProbeSetXRef AS t ON t.Symbol = x.Symbol "
+                "AND t.Mean = x.maxmean")
+            cursor.execute(
+                query, probeset_freeze_id=probeset_freeze_id,
+                symbols=tuple(gene_name_list))
+
+        results = cursor.fetchall()
+
+    return reduce(
+        lambda acc, item: (
+            acc[0] + (item[0],),
+            {**acc[1], item[0].lower(): item[1]},
+            {**acc[1], item[0].lower(): item[2]},
+            {**acc[1], item[0].lower(): item[3]},
+            {**acc[1], item[0].lower(): item[4]},
+            {**acc[1], item[0].lower(): item[5]},
+            {**acc[1], item[0].lower(): item[6]}),
+        results or tuple(),
+        (tuple(), {}, {}, {}, {}, {}, {}))
+
+def fetch_gene_symbol_tissue_value_dict_for_trait(
+        gene_name_list: Tuple[str, ...], probeset_freeze_id: int,
+        conn: Any) -> dict:
+    """
+    Fetches a map of the gene symbols to the tissue values.
+
+    This is a migration of the
+    `web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDictForTrait`
+    function in GeneNetwork1.
+    """
+    xref_info = fetch_tissue_probeset_xref_info(
+        gene_name_list, probeset_freeze_id, conn)
+    if xref_info[0]:
+        return fetch_gene_symbol_tissue_value_dict(xref_info[0], xref_info[2], conn)
+    return {}
+
+def build_temporary_tissue_correlations_table(
+        conn: Any, trait_symbol: str, probeset_freeze_id: int, method: str,
+        return_number: int) -> str:
+    """
+    Build a temporary table to hold the tissue correlations data.
+
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.getTempTissueCorrTable` function in
+    GeneNetwork1."""
+    # We should probably pass the `correlations_of_all_tissue_traits` function
+    # as an argument to this function and get rid of the one call immediately
+    # following this comment.
+    from gn3.computations.partial_correlations import (#pylint: disable=[C0415, R0401]
+        correlations_of_all_tissue_traits)
+    # This import above is necessary within the function to avoid
+    # circular-imports.
+    #
+    #
+    # This import above is indicative of convoluted code, with the computation
+    # being interwoven with the data retrieval. This needs to be changed, such
+    # that the function being imported here is no longer necessary, or have the
+    # imported function passed to this function as an argument.
+    symbol_corr_dict, symbol_p_value_dict = correlations_of_all_tissue_traits(
+        fetch_gene_symbol_tissue_value_dict_for_trait(
+            (trait_symbol,), probeset_freeze_id, conn),
+        fetch_gene_symbol_tissue_value_dict_for_trait(
+            tuple(), probeset_freeze_id, conn),
+        method)
+
+    symbol_corr_list = sorted(
+        symbol_corr_dict.items(), key=lambda key_val: key_val[1])
+
+    temp_table_name = f"TOPTISSUE{random_string(8)}"
+    create_query = (
+        "CREATE TEMPORARY TABLE {temp_table_name}"
+        "(Symbol varchar(100) PRIMARY KEY, Correlation float, PValue float)")
+    insert_query = (
+        f"INSERT INTO {temp_table_name}(Symbol, Correlation, PValue) "
+        " VALUES (%(symbol)s, %(correlation)s, %(pvalue)s)")
+
+    with conn.cursor() as cursor:
+        cursor.execute(create_query)
+        cursor.execute(
+            insert_query,
+            tuple({
+                "symbol": symbol,
+                "correlation": corr,
+                "pvalue": symbol_p_value_dict[symbol]
+            } for symbol, corr in symbol_corr_list[0: 2 * return_number]))
+
+    return temp_table_name
+
+def fetch_tissue_correlations(# pylint: disable=R0913
+        dataset: dict, trait_symbol: str, probeset_freeze_id: int, method: str,
+        return_number: int, conn: Any) -> dict:
+    """
+    Pair tissue correlations data with a trait id string.
+
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.fetchTissueCorrelations` function in
+    GeneNetwork1.
+    """
+    temp_table = build_temporary_tissue_correlations_table(
+        conn, trait_symbol, probeset_freeze_id, method, return_number)
+    with conn.cursor() as cursor:
+        cursor.execute(
+            (
+                f"SELECT ProbeSet.Name, {temp_table}.Correlation, "
+                f"{temp_table}.PValue "
+                "FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) "
+                "LEFT JOIN {temp_table} ON {temp_table}.Symbol=ProbeSet.Symbol "
+                "WHERE ProbeSetFreeze.Name = %(db_name) "
+                "AND ProbeSetFreeze.Id=ProbeSetXRef.ProbeSetFreezeId "
+                "AND ProbeSet.Id = ProbeSetXRef.ProbeSetId "
+                "AND ProbeSet.Symbol IS NOT NULL "
+                "AND %s.Correlation IS NOT NULL"),
+            db_name=dataset["dataset_name"])
+        results = cursor.fetchall()
+        cursor.execute("DROP TEMPORARY TABLE %s", temp_table)
+        return {
+            trait_name: (tiss_corr, tiss_p_val)
+            for trait_name, tiss_corr, tiss_p_val in results}
+
+def check_for_literature_info(conn: Any, geneid: int) -> bool:
+    """
+    Checks the database to find out whether the trait with `geneid` has any
+    associated literature.
+
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.checkForLitInfo` function in
+    GeneNetwork1.
+    """
+    query = "SELECT 1 FROM LCorrRamin3 WHERE GeneId1=%s LIMIT 1"
+    with conn.cursor() as cursor:
+        cursor.execute(query, geneid)
+        result = cursor.fetchone()
+        if result:
+            return True
+
+    return False
+
+def check_symbol_for_tissue_correlation(
+        conn: Any, tissue_probeset_freeze_id: int, symbol: str = "") -> bool:
+    """
+    Checks whether a symbol has any associated tissue correlations.
+
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.checkSymbolForTissueCorr` function
+    in GeneNetwork1.
+    """
+    query = (
+        "SELECT 1 FROM  TissueProbeSetXRef "
+        "WHERE TissueProbeSetFreezeId=%(probeset_freeze_id)s "
+        "AND Symbol=%(symbol)s LIMIT 1")
+    with conn.cursor() as cursor:
+        cursor.execute(
+            query, probeset_freeze_id=tissue_probeset_freeze_id, symbol=symbol)
+        result = cursor.fetchone()
+        if result:
+            return True
+
+    return False
+
+def fetch_sample_ids(
+        conn: Any, sample_names: Tuple[str, ...], species_name: str) -> Tuple[
+            int, ...]:
+    """
+    Given a sequence of sample names, and a species name, return the sample ids
+    that correspond to both.
+
+    This is a partial migration of the
+    `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function in
+    GeneNetwork1.
+    """
+    query = (
+        "SELECT Strain.Id FROM Strain, Species "
+        "WHERE Strain.Name IN %(samples_names)s "
+        "AND Strain.SpeciesId=Species.Id "
+        "AND Species.name=%(species_name)s")
+    with conn.cursor() as cursor:
+        cursor.execute(
+            query,
+            {
+                "samples_names": tuple(sample_names),
+                "species_name": species_name
+            })
+        return tuple(row[0] for row in cursor.fetchall())
+
+def build_query_sgo_lit_corr(
+        db_type: str, temp_table: str, sample_id_columns: str,
+        joins: Tuple[str, ...]) -> str:
+    """
+    Build query for `SGO Literature Correlation` data, when querying the given
+    `temp_table` temporary table.
+
+    This is a partial migration of the
+    `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function in
+    GeneNetwork1.
+    """
+    return (
+        (f"SELECT {db_type}.Name, {temp_table}.value, " +
+         sample_id_columns +
+         f" FROM ({db_type}, {db_type}XRef, {db_type}Freeze) " +
+         f"LEFT JOIN {temp_table} ON {temp_table}.GeneId2=ProbeSet.GeneId " +
+         " ".join(joins) +
+         " WHERE ProbeSet.GeneId IS NOT NULL " +
+         f"AND {temp_table}.value IS NOT NULL " +
+         f"AND {db_type}XRef.{db_type}FreezeId = {db_type}Freeze.Id " +
+         f"AND {db_type}Freeze.Name = %(db_name)s " +
+         f"AND {db_type}.Id = {db_type}XRef.{db_type}Id " +
+         f"ORDER BY {db_type}.Id"),
+        2)
+
+def build_query_tissue_corr(db_type, temp_table, sample_id_columns, joins):
+    """
+    Build query for `Tissue Correlation` data, when querying the given
+    `temp_table` temporary table.
+
+    This is a partial migration of the
+    `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function in
+    GeneNetwork1.
+    """
+    return (
+        (f"SELECT {db_type}.Name, {temp_table}.Correlation, " +
+         f"{temp_table}.PValue, " +
+         sample_id_columns +
+         f" FROM ({db_type}, {db_type}XRef, {db_type}Freeze) " +
+         f"LEFT JOIN {temp_table} ON {temp_table}.Symbol=ProbeSet.Symbol " +
+         " ".join(joins) +
+         " WHERE ProbeSet.Symbol IS NOT NULL " +
+         f"AND {temp_table}.Correlation IS NOT NULL " +
+         f"AND {db_type}XRef.{db_type}FreezeId = {db_type}Freeze.Id " +
+         f"AND {db_type}Freeze.Name = %(db_name)s " +
+         f"AND {db_type}.Id = {db_type}XRef.{db_type}Id "
+         f"ORDER BY {db_type}.Id"),
+        3)
+
+def fetch_all_database_data(# pylint: disable=[R0913, R0914]
+        conn: Any, species: str, gene_id: int, trait_symbol: str,
+        samples: Tuple[str, ...], dataset: dict, method: str,
+        return_number: int, probeset_freeze_id: int) -> Tuple[
+            Tuple[float], int]:
+    """
+    This is a migration of the
+    `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function in
+    GeneNetwork1.
+    """
+    db_type = dataset["dataset_type"]
+    db_name = dataset["dataset_name"]
+    def __build_query__(sample_ids, temp_table):
+        sample_id_columns = ", ".join(f"T{smpl}.value" for smpl in sample_ids)
+        if db_type == "Publish":
+            joins = tuple(
+                ("LEFT JOIN PublishData AS T{item} "
+                 "ON T{item}.Id = PublishXRef.DataId "
+                 "AND T{item}.StrainId = %(T{item}_sample_id)s")
+                for item in sample_ids)
+            return (
+                ("SELECT PublishXRef.Id, " +
+                 sample_id_columns +
+                 "FROM (PublishXRef, PublishFreeze) " +
+                 " ".join(joins) +
+                 " WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId "
+                 "AND PublishFreeze.Name = %(db_name)s"),
+                1)
+        if temp_table is not None:
+            joins = tuple(
+                (f"LEFT JOIN {db_type}Data AS T{item} "
+                 f"ON T{item}.Id = {db_type}XRef.DataId "
+                 f"AND T{item}.StrainId=%(T{item}_sample_id)s")
+                for item in sample_ids)
+            if method.lower() == "sgo literature correlation":
+                return build_query_sgo_lit_corr(
+                    sample_ids, temp_table, sample_id_columns, joins)
+            if method.lower() in (
+                    "tissue correlation, pearson's r",
+                    "tissue correlation, spearman's rho"):
+                return build_query_tissue_corr(
+                    sample_ids, temp_table, sample_id_columns, joins)
+        joins = tuple(
+            (f"LEFT JOIN {db_type}Data AS T{item} "
+             f"ON T{item}.Id = {db_type}XRef.DataId "
+             f"AND T{item}.StrainId = %(T{item}_sample_id)s")
+            for item in sample_ids)
+        return (
+            (
+                f"SELECT {db_type}.Name, " +
+                sample_id_columns +
+                f" FROM ({db_type}, {db_type}XRef, {db_type}Freeze) " +
+                " ".join(joins) +
+                f" WHERE {db_type}XRef.{db_type}FreezeId = {db_type}Freeze.Id " +
+                f"AND {db_type}Freeze.Name = %(db_name)s " +
+                f"AND {db_type}.Id = {db_type}XRef.{db_type}Id " +
+                f"ORDER BY {db_type}.Id"),
+            1)
+
+    def __fetch_data__(sample_ids, temp_table):
+        query, data_start_pos = __build_query__(sample_ids, temp_table)
+        with conn.cursor() as cursor:
+            cursor.execute(
+                query,
+                {"db_name": db_name,
+                 **{f"T{item}_sample_id": item for item in sample_ids}})
+            return (cursor.fetchall(), data_start_pos)
+
+    sample_ids = tuple(
+        # look into graduating this to an argument and removing the `samples`
+        # and `species` argument: function currying and compositions might help
+        # with this
+        f"{sample_id}" for sample_id in
+        fetch_sample_ids(conn, samples, species))
+
+    temp_table = None
+    if gene_id and db_type == "probeset":
+        if method.lower() == "sgo literature correlation":
+            temp_table = build_temporary_literature_table(
+                conn, species, gene_id, return_number)
+        if method.lower() in (
+                "tissue correlation, pearson's r",
+                "tissue correlation, spearman's rho"):
+            temp_table = build_temporary_tissue_correlations_table(
+                conn, trait_symbol, probeset_freeze_id, method, return_number)
+
+    trait_database = tuple(
+        item for sublist in
+        (__fetch_data__(ssample_ids, temp_table)
+         for ssample_ids in partition_all(25, sample_ids))
+        for item in sublist)
+
+    if temp_table:
+        with conn.cursor() as cursor:
+            cursor.execute(f"DROP TEMPORARY TABLE {temp_table}")
+
+    return (trait_database[0], trait_database[1])
diff --git a/gn3/db/species.py b/gn3/db/species.py
index 0deae4e..5b8e096 100644
--- a/gn3/db/species.py
+++ b/gn3/db/species.py
@@ -30,3 +30,47 @@ def get_chromosome(name: str, is_species: bool, conn: Any) -> Optional[Tuple]:
     with conn.cursor() as cursor:
         cursor.execute(_sql)
         return cursor.fetchall()
+
+def translate_to_mouse_gene_id(species: str, geneid: int, conn: Any) -> int:
+    """
+    Translate rat or human geneid to mouse geneid
+
+    This is a migration of the
+    `web.webqtl.correlation/CorrelationPage.translateToMouseGeneID` function in
+    GN1
+    """
+    assert species in ("rat", "mouse", "human"), "Invalid species"
+    if geneid is None:
+        return 0
+
+    if species == "mouse":
+        return geneid
+
+    with conn.cursor as cursor:
+        query = {
+            "rat": "SELECT mouse FROM GeneIDXRef WHERE rat = %s",
+            "human": "SELECT mouse FROM GeneIDXRef WHERE human = %s"
+        }
+        cursor.execute(query[species], geneid)
+        translated_gene_id = cursor.fetchone()
+        if translated_gene_id:
+            return translated_gene_id[0]
+
+    return 0 # default if all else fails
+
+def species_name(conn: Any, group: str) -> str:
+    """
+    Retrieve the name of the species, given the group (RISet).
+
+    This is a migration of the
+    `web.webqtl.dbFunction.webqtlDatabaseFunction.retrieveSpecies` function in
+    GeneNetwork1.
+    """
+    with conn.cursor() as cursor:
+        cursor.execute(
+            ("SELECT Species.Name FROM Species, InbredSet "
+             "WHERE InbredSet.Name = %(group_name)s "
+             "AND InbredSet.SpeciesId = Species.Id"),
+            {"group_name": group})
+        return cursor.fetchone()[0]
+    return None
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index f2673c8..4098b08 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,17 +1,93 @@
 """This class contains functions relating to trait data manipulation"""
 import os
+import MySQLdb
+from functools import reduce
 from typing import Any, Dict, Union, Sequence
+
+import MySQLdb
+
 from gn3.settings import TMPDIR
 from gn3.random import random_string
 from gn3.function_helpers import compose
 from gn3.db.datasets import retrieve_trait_dataset
 
 
+def export_trait_data(
+        trait_data: dict, samplelist: Sequence[str], dtype: str = "val",
+        var_exists: bool = False, n_exists: bool = False):
+    """
+    Export data according to `samplelist`. Mostly used in calculating
+    correlations.
+
+    DESCRIPTION:
+    Migrated from
+    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L166-L211
+
+    PARAMETERS
+    trait: (dict)
+      The dictionary of key-value pairs representing a trait
+    samplelist: (list)
+      A list of sample names
+    dtype: (str)
+      ... verify what this is ...
+    var_exists: (bool)
+      A flag indicating existence of variance
+    n_exists: (bool)
+      A flag indicating existence of ndata
+    """
+    def __export_all_types(tdata, sample):
+        sample_data = []
+        if tdata[sample]["value"]:
+            sample_data.append(tdata[sample]["value"])
+            if var_exists:
+                if tdata[sample]["variance"]:
+                    sample_data.append(tdata[sample]["variance"])
+                else:
+                    sample_data.append(None)
+            if n_exists:
+                if tdata[sample]["ndata"]:
+                    sample_data.append(tdata[sample]["ndata"])
+                else:
+                    sample_data.append(None)
+        else:
+            if var_exists and n_exists:
+                sample_data += [None, None, None]
+            elif var_exists or n_exists:
+                sample_data += [None, None]
+            else:
+                sample_data.append(None)
+
+        return tuple(sample_data)
+
+    def __exporter(accumulator, sample):
+        # pylint: disable=[R0911]
+        if sample in trait_data["data"]:
+            if dtype == "val":
+                return accumulator + (trait_data["data"][sample]["value"], )
+            if dtype == "var":
+                return accumulator + (trait_data["data"][sample]["variance"], )
+            if dtype == "N":
+                return accumulator + (trait_data["data"][sample]["ndata"], )
+            if dtype == "all":
+                return accumulator + __export_all_types(trait_data["data"], sample)
+            raise KeyError("Type `%s` is incorrect" % dtype)
+        if var_exists and n_exists:
+            return accumulator + (None, None, None)
+        if var_exists or n_exists:
+            return accumulator + (None, None)
+        return accumulator + (None,)
+
+    return reduce(__exporter, samplelist, tuple())
+
+
 def get_trait_csv_sample_data(conn: Any,
                               trait_name: int, phenotype_id: int):
     """Fetch a trait and return it as a csv string"""
-    sql = ("SELECT DISTINCT Strain.Id, PublishData.Id, Strain.Name, "
-           "PublishData.value, "
+    def __float_strip(num_str):
+        if str(num_str)[-2:] == ".0":
+            return str(int(num_str))
+        return str(num_str)
+    sql = ("SELECT DISTINCT Strain.Name, PublishData.value, "
            "PublishSE.error, NStrain.count FROM "
            "(PublishData, Strain, PublishXRef, PublishFreeze) "
            "LEFT JOIN PublishSE ON "
@@ -23,65 +99,189 @@ def get_trait_csv_sample_data(conn: Any,
            "PublishData.Id = PublishXRef.DataId AND "
            "PublishXRef.Id = %s AND PublishXRef.PhenotypeId = %s "
            "AND PublishData.StrainId = Strain.Id Order BY Strain.Name")
-    csv_data = ["Strain Id,Strain Name,Value,SE,Count"]
-    publishdata_id = ""
+    csv_data = ["Strain Name,Value,SE,Count"]
     with conn.cursor() as cursor:
         cursor.execute(sql, (trait_name, phenotype_id,))
         for record in cursor.fetchall():
-            (strain_id, publishdata_id,
-             strain_name, value, error, count) = record
+            (strain_name, value, error, count) = record
             csv_data.append(
-                ",".join([str(val) if val else "x"
-                          for val in (strain_id, strain_name,
-                                      value, error, count)]))
-    return f"# Publish Data Id: {publishdata_id}\n\n" + "\n".join(csv_data)
+                ",".join([__float_strip(val) if val else "x"
+                          for val in (strain_name, value, error, count)]))
+    return "\n".join(csv_data)
+
 
+def update_sample_data(conn: Any, #pylint: disable=[R0913]
 
-def update_sample_data(conn: Any,
+                       trait_name: str,
                        strain_name: str,
-                       strain_id: int,
-                       publish_data_id: int,
+                       phenotype_id: int,
                        value: Union[int, float, str],
                        error: Union[int, float, str],
                        count: Union[int, str]):
     """Given the right parameters, update sample-data from the relevant
     table."""
-    # pylint: disable=[R0913, R0914, C0103]
-    STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s"
-    PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s "
-                             "WHERE StrainId = %s AND Id = %s")
-    PUBLISH_SE_SQL: str = ("UPDATE PublishSE SET error = %s "
-                           "WHERE StrainId = %s AND DataId = %s")
-    N_STRAIN_SQL: str = ("UPDATE NStrain SET count = %s "
-                         "WHERE StrainId = %s AND DataId = %s")
-
-    updated_strains: int = 0
+    strain_id, data_id = "", ""
+
+    with conn.cursor() as cursor:
+        cursor.execute(
+            ("SELECT Strain.Id, PublishData.Id 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 "
+             "PublishXRef.PhenotypeId = %s "
+             "AND PublishData.StrainId = Strain.Id "
+             "AND Strain.Name = \"%s\"") % (trait_name,
+                                            phenotype_id,
+                                            str(strain_name)))
+        strain_id, data_id = cursor.fetchone()
     updated_published_data: int = 0
     updated_se_data: int = 0
     updated_n_strains: int = 0
 
     with conn.cursor() as cursor:
-        # Update the Strains table
-        cursor.execute(STRAIN_ID_SQL, (strain_name, strain_id))
-        updated_strains = cursor.rowcount
         # Update the PublishData table
-        cursor.execute(PUBLISH_DATA_SQL,
+        cursor.execute(("UPDATE PublishData SET value = %s "
+                        "WHERE StrainId = %s AND Id = %s"),
                        (None if value == "x" else value,
-                        strain_id, publish_data_id))
+                        strain_id, data_id))
         updated_published_data = cursor.rowcount
+
         # Update the PublishSE table
-        cursor.execute(PUBLISH_SE_SQL,
+        cursor.execute(("UPDATE PublishSE SET error = %s "
+                        "WHERE StrainId = %s AND DataId = %s"),
                        (None if error == "x" else error,
-                        strain_id, publish_data_id))
+                        strain_id, data_id))
         updated_se_data = cursor.rowcount
+
         # Update the NStrain table
-        cursor.execute(N_STRAIN_SQL,
+        cursor.execute(("UPDATE NStrain SET count = %s "
+                        "WHERE StrainId = %s AND DataId = %s"),
                        (None if count == "x" else count,
-                        strain_id, publish_data_id))
+                        strain_id, data_id))
         updated_n_strains = cursor.rowcount
-    return (updated_strains, updated_published_data,
+    return (updated_published_data,
             updated_se_data, updated_n_strains)
 
+
+def delete_sample_data(conn: Any,
+                       trait_name: str,
+                       strain_name: str,
+                       phenotype_id: int):
+    """Given the right parameters, delete sample-data from the relevant
+    table."""
+    strain_id, data_id = "", ""
+
+    deleted_published_data: int = 0
+    deleted_se_data: int = 0
+    deleted_n_strains: int = 0
+
+    with conn.cursor() as cursor:
+        # Delete the PublishData table
+        try:
+            cursor.execute(
+                ("SELECT Strain.Id, PublishData.Id 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 "
+                 "PublishXRef.PhenotypeId = %s "
+                 "AND PublishData.StrainId = Strain.Id "
+                 "AND Strain.Name = \"%s\"") % (trait_name,
+                                                phenotype_id,
+                                                str(strain_name)))
+            strain_id, data_id = cursor.fetchone()
+
+            cursor.execute(("DELETE FROM PublishData "
+                            "WHERE StrainId = %s AND Id = %s")
+                           % (strain_id, data_id))
+            deleted_published_data = cursor.rowcount
+
+            # Delete the PublishSE table
+            cursor.execute(("DELETE FROM PublishSE "
+                            "WHERE StrainId = %s AND DataId = %s") %
+                           (strain_id, data_id))
+            deleted_se_data = cursor.rowcount
+
+            # Delete the NStrain table
+            cursor.execute(("DELETE FROM NStrain "
+                            "WHERE StrainId = %s AND DataId = %s" %
+                            (strain_id, data_id)))
+            deleted_n_strains = cursor.rowcount
+        except Exception as e: #pylint: disable=[C0103, W0612]
+            conn.rollback()
+            raise MySQLdb.Error
+        conn.commit()
+        cursor.close()
+        cursor.close()
+
+    return (deleted_published_data,
+            deleted_se_data, deleted_n_strains)
+
+
+def insert_sample_data(conn: Any, #pylint: disable=[R0913]
+                       trait_name: str,
+                       strain_name: str,
+                       phenotype_id: int,
+                       value: Union[int, float, str],
+                       error: Union[int, float, str],
+                       count: Union[int, str]):
+    """Given the right parameters, insert sample-data to the relevant table.
+
+    """
+
+    inserted_published_data, inserted_se_data, inserted_n_strains = 0, 0, 0
+    with conn.cursor() as cursor:
+        try:
+            cursor.execute("SELECT DataId FROM PublishXRef WHERE Id = %s AND "
+                           "PhenotypeId = %s", (trait_name, phenotype_id))
+            data_id = cursor.fetchone()
+
+            cursor.execute("SELECT Id FROM Strain WHERE Name = %s",
+                           (strain_name,))
+            strain_id = cursor.fetchone()
+
+            # Insert the PublishData table
+            cursor.execute(("INSERT INTO PublishData (Id, StrainId, value)"
+                            "VALUES (%s, %s, %s)"),
+                           (data_id, strain_id, value))
+            inserted_published_data = cursor.rowcount
+
+            # Insert into the PublishSE table if error is specified
+            if error and error != "x":
+                cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, "
+                                " error) VALUES (%s, %s, %s)") %
+                               (strain_id, data_id, error))
+            inserted_se_data = cursor.rowcount
+
+            # Insert into the NStrain table
+            if count and count != "x":
+                cursor.execute(("INSERT INTO NStrain "
+                                "(StrainId, DataId, error) "
+                                "VALUES (%s, %s, %s)") %
+                               (strain_id, data_id, count))
+            inserted_n_strains = cursor.rowcount
+        except Exception as e: #pylint: disable=[C0103, W0612]
+            conn.rollback()
+            raise MySQLdb.Error
+    return (inserted_published_data,
+            inserted_se_data, inserted_n_strains)
+
+
 def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
     """Retrieve trait information for type `Publish` traits.
 
@@ -121,11 +321,12 @@ def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
         cursor.execute(
             query,
             {
-                k:v for k, v in trait_data_source.items()
+                k: v for k, v in trait_data_source.items()
                 if k in ["trait_name", "trait_dataset_id"]
             })
         return dict(zip([k.lower() for k in keys], cursor.fetchone()))
 
+
 def set_confidential_field(trait_type, trait_info):
     """Post processing function for 'Publish' trait types.
 
@@ -138,6 +339,7 @@ def set_confidential_field(trait_type, trait_info):
                 and not trait_info.get("pubmed_id", None)) else 0}
     return trait_info
 
+
 def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
     """Retrieve trait information for type `ProbeSet` traits.
 
@@ -165,11 +367,12 @@ def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
         cursor.execute(
             query,
             {
-                k:v for k, v in trait_data_source.items()
+                k: v for k, v in trait_data_source.items()
                 if k in ["trait_name", "trait_dataset_name"]
             })
         return dict(zip(keys, cursor.fetchone()))
 
+
 def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any):
     """Retrieve trait information for type `Geno` traits.
 
@@ -189,11 +392,12 @@ def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any):
         cursor.execute(
             query,
             {
-                k:v for k, v in trait_data_source.items()
+                k: v for k, v in trait_data_source.items()
                 if k in ["trait_name", "trait_dataset_name"]
             })
         return dict(zip(keys, cursor.fetchone()))
 
+
 def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
     """Retrieve trait information for type `Temp` traits.
 
@@ -206,11 +410,12 @@ def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
         cursor.execute(
             query,
             {
-                k:v for k, v in trait_data_source.items()
+                k: v for k, v in trait_data_source.items()
                 if k in ["trait_name"]
             })
         return dict(zip(keys, cursor.fetchone()))
 
+
 def set_haveinfo_field(trait_info):
     """
     Common postprocessing function for all trait types.
@@ -218,6 +423,7 @@ def set_haveinfo_field(trait_info):
     Sets the value for the 'haveinfo' field."""
     return {**trait_info, "haveinfo": 1 if trait_info else 0}
 
+
 def set_homologene_id_field_probeset(trait_info, conn):
     """
     Postprocessing function for 'ProbeSet' traits.
@@ -233,7 +439,7 @@ def set_homologene_id_field_probeset(trait_info, conn):
         cursor.execute(
             query,
             {
-                k:v for k, v in trait_info.items()
+                k: v for k, v in trait_info.items()
                 if k in ["geneid", "group"]
             })
         res = cursor.fetchone()
@@ -241,12 +447,13 @@ def set_homologene_id_field_probeset(trait_info, conn):
             return {**trait_info, "homologeneid": res[0]}
     return {**trait_info, "homologeneid": None}
 
+
 def set_homologene_id_field(trait_type, trait_info, conn):
     """
     Common postprocessing function for all trait types.
 
     Sets the value for the 'homologene' key."""
-    set_to_null = lambda ti: {**ti, "homologeneid": None}
+    def set_to_null(ti): return {**ti, "homologeneid": None} # pylint: disable=[C0103, C0321]
     functions_table = {
         "Temp": set_to_null,
         "Geno": set_to_null,
@@ -255,6 +462,7 @@ def set_homologene_id_field(trait_type, trait_info, conn):
     }
     return functions_table[trait_type](trait_info)
 
+
 def load_publish_qtl_info(trait_info, conn):
     """
     Load extra QTL information for `Publish` traits
@@ -275,6 +483,7 @@ def load_publish_qtl_info(trait_info, conn):
         return dict(zip(["locus", "lrs", "additive"], cursor.fetchone()))
     return {"locus": "", "lrs": "", "additive": ""}
 
+
 def load_probeset_qtl_info(trait_info, conn):
     """
     Load extra QTL information for `ProbeSet` traits
@@ -297,6 +506,7 @@ def load_probeset_qtl_info(trait_info, conn):
             ["locus", "lrs", "pvalue", "mean", "additive"], cursor.fetchone()))
     return {"locus": "", "lrs": "", "pvalue": "", "mean": "", "additive": ""}
 
+
 def load_qtl_info(qtl, trait_type, trait_info, conn):
     """
     Load extra QTL information for traits
@@ -325,6 +535,7 @@ def load_qtl_info(qtl, trait_type, trait_info, conn):
 
     return qtl_info_functions[trait_type](trait_info, conn)
 
+
 def build_trait_name(trait_fullname):
     """
     Initialises the trait's name, and other values from the search data provided
@@ -351,6 +562,7 @@ def build_trait_name(trait_fullname):
         "cellid": name_parts[2] if len(name_parts) == 3 else ""
     }
 
+
 def retrieve_probeset_sequence(trait, conn):
     """
     Retrieve a 'ProbeSet' trait's sequence information
@@ -372,6 +584,7 @@ def retrieve_probeset_sequence(trait, conn):
         seq = cursor.fetchone()
         return {**trait, "sequence": seq[0] if seq else ""}
 
+
 def retrieve_trait_info(
         threshold: int, trait_full_name: str, conn: Any,
         qtl=None):
@@ -427,6 +640,7 @@ def retrieve_trait_info(
         }
     return trait_info
 
+
 def retrieve_temp_trait_data(trait_info: dict, conn: Any):
     """
     Retrieve trait data for `Temp` traits.
@@ -445,10 +659,12 @@ def retrieve_temp_trait_data(trait_info: dict, conn: Any):
             query,
             {"trait_name": trait_info["trait_name"]})
         return [dict(zip(
-            ["sample_name", "value", "se_error", "nstrain", "id"], row))
+            ["sample_name", "value", "se_error", "nstrain", "id"],
+            row))
                 for row in cursor.fetchall()]
     return []
 
+
 def retrieve_species_id(group, conn: Any):
     """
     Retrieve a species id given the Group value
@@ -460,6 +676,7 @@ def retrieve_species_id(group, conn: Any):
         return cursor.fetchone()[0]
     return None
 
+
 def retrieve_geno_trait_data(trait_info: Dict, conn: Any):
     """
     Retrieve trait data for `Geno` traits.
@@ -483,11 +700,14 @@ def retrieve_geno_trait_data(trait_info: Dict, conn: Any):
              "dataset_name": trait_info["db"]["dataset_name"],
              "species_id": retrieve_species_id(
                  trait_info["db"]["group"], conn)})
-        return [dict(zip(
-            ["sample_name", "value", "se_error", "id"], row))
-                for row in cursor.fetchall()]
+        return [
+            dict(zip(
+                ["sample_name", "value", "se_error", "id"],
+                row))
+            for row in cursor.fetchall()]
     return []
 
+
 def retrieve_publish_trait_data(trait_info: Dict, conn: Any):
     """
     Retrieve trait data for `Publish` traits.
@@ -514,11 +734,13 @@ def retrieve_publish_trait_data(trait_info: Dict, conn: Any):
             query,
             {"trait_name": trait_info["trait_name"],
              "dataset_id": trait_info["db"]["dataset_id"]})
-        return [dict(zip(
-            ["sample_name", "value", "se_error", "nstrain", "id"], row))
-                for row in cursor.fetchall()]
+        return [
+            dict(zip(
+                ["sample_name", "value", "se_error", "nstrain", "id"], row))
+            for row in cursor.fetchall()]
     return []
 
+
 def retrieve_cellid_trait_data(trait_info: Dict, conn: Any):
     """
     Retrieve trait data for `Probe Data` types.
@@ -547,11 +769,13 @@ def retrieve_cellid_trait_data(trait_info: Dict, conn: Any):
             {"cellid": trait_info["cellid"],
              "trait_name": trait_info["trait_name"],
              "dataset_id": trait_info["db"]["dataset_id"]})
-        return [dict(zip(
-            ["sample_name", "value", "se_error", "id"], row))
-                for row in cursor.fetchall()]
+        return [
+            dict(zip(
+                ["sample_name", "value", "se_error", "id"], row))
+            for row in cursor.fetchall()]
     return []
 
+
 def retrieve_probeset_trait_data(trait_info: Dict, conn: Any):
     """
     Retrieve trait data for `ProbeSet` traits.
@@ -576,11 +800,13 @@ def retrieve_probeset_trait_data(trait_info: Dict, conn: Any):
             query,
             {"trait_name": trait_info["trait_name"],
              "dataset_name": trait_info["db"]["dataset_name"]})
-        return [dict(zip(
-            ["sample_name", "value", "se_error", "id"], row))
-                for row in cursor.fetchall()]
+        return [
+            dict(zip(
+                ["sample_name", "value", "se_error", "id"], row))
+            for row in cursor.fetchall()]
     return []
 
+
 def with_samplelist_data_setup(samplelist: Sequence[str]):
     """
     Build function that computes the trait data from provided list of samples.
@@ -607,6 +833,7 @@ def with_samplelist_data_setup(samplelist: Sequence[str]):
         return None
     return setup_fn
 
+
 def without_samplelist_data_setup():
     """
     Build function that computes the trait data.
@@ -627,6 +854,7 @@ def without_samplelist_data_setup():
         return None
     return setup_fn
 
+
 def retrieve_trait_data(trait: dict, conn: Any, samplelist: Sequence[str] = tuple()):
     """
     Retrieve trait data
@@ -666,11 +894,38 @@ def retrieve_trait_data(trait: dict, conn: Any, samplelist: Sequence[str] = tupl
             "data": dict(map(
                 lambda x: (
                     x["sample_name"],
-                    {k:v for k, v in x.items() if x != "sample_name"}),
+                    {k: v for k, v in x.items() if x != "sample_name"}),
                 data))}
     return {}
 
+
 def generate_traits_filename(base_path: str = TMPDIR):
     """Generate a unique filename for use with generated traits files."""
     return "{}/traits_test_file_{}.txt".format(
         os.path.abspath(base_path), random_string(10))
+
+
+def export_informative(trait_data: dict, inc_var: bool = False) -> tuple:
+    """
+    Export informative strain
+
+    This is a migration of the `exportInformative` function in
+    web/webqtl/base/webqtlTrait.py module in GeneNetwork1.
+
+    There is a chance that the original implementation has a bug, especially
+    dealing with the `inc_var` value. It the `inc_var` value is meant to control
+    the inclusion of the `variance` value, then the current implementation, and
+    that one in GN1 have a bug.
+    """
+    def __exporter__(acc, data_item):
+        if not inc_var or data_item["variance"] is not None:
+            return (
+                acc[0] + (data_item["sample_name"],),
+                acc[1] + (data_item["value"],),
+                acc[2] + (data_item["variance"],))
+        return acc
+    return reduce(
+        __exporter__,
+        filter(lambda td: td["value"] is not None,
+               trait_data["data"].values()),
+        (tuple(), tuple(), tuple()))
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index adbfbc6..f0af409 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -14,6 +14,7 @@ from plotly.subplots import make_subplots # type: ignore
 from gn3.settings import TMPDIR
 from gn3.random import random_string
 from gn3.computations.slink import slink
+from gn3.db.traits import export_trait_data
 from gn3.computations.correlations2 import compute_correlation
 from gn3.db.genotypes import (
     build_genotype_file, load_genotype_samples)
@@ -26,72 +27,6 @@ from gn3.computations.qtlreaper import (
     parse_reaper_main_results,
     organise_reaper_main_results)
 
-def export_trait_data(
-        trait_data: dict, samplelist: Sequence[str], dtype: str = "val",
-        var_exists: bool = False, n_exists: bool = False):
-    """
-    Export data according to `samplelist`. Mostly used in calculating
-    correlations.
-
-    DESCRIPTION:
-    Migrated from
-    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L166-L211
-
-    PARAMETERS
-    trait: (dict)
-      The dictionary of key-value pairs representing a trait
-    samplelist: (list)
-      A list of sample names
-    dtype: (str)
-      ... verify what this is ...
-    var_exists: (bool)
-      A flag indicating existence of variance
-    n_exists: (bool)
-      A flag indicating existence of ndata
-    """
-    def __export_all_types(tdata, sample):
-        sample_data = []
-        if tdata[sample]["value"]:
-            sample_data.append(tdata[sample]["value"])
-            if var_exists:
-                if tdata[sample]["variance"]:
-                    sample_data.append(tdata[sample]["variance"])
-                else:
-                    sample_data.append(None)
-            if n_exists:
-                if tdata[sample]["ndata"]:
-                    sample_data.append(tdata[sample]["ndata"])
-                else:
-                    sample_data.append(None)
-        else:
-            if var_exists and n_exists:
-                sample_data += [None, None, None]
-            elif var_exists or n_exists:
-                sample_data += [None, None]
-            else:
-                sample_data.append(None)
-
-        return tuple(sample_data)
-
-    def __exporter(accumulator, sample):
-        # pylint: disable=[R0911]
-        if sample in trait_data["data"]:
-            if dtype == "val":
-                return accumulator + (trait_data["data"][sample]["value"], )
-            if dtype == "var":
-                return accumulator + (trait_data["data"][sample]["variance"], )
-            if dtype == "N":
-                return accumulator + (trait_data["data"][sample]["ndata"], )
-            if dtype == "all":
-                return accumulator + __export_all_types(trait_data["data"], sample)
-            raise KeyError("Type `%s` is incorrect" % dtype)
-        if var_exists and n_exists:
-            return accumulator + (None, None, None)
-        if var_exists or n_exists:
-            return accumulator + (None, None)
-        return accumulator + (None,)
-
-    return reduce(__exporter, samplelist, tuple())
 
 def trait_display_name(trait: Dict):
     """
@@ -129,11 +64,7 @@ def cluster_traits(traits_data_list: Sequence[Dict]):
     def __compute_corr(tdata_i, tdata_j):
         if tdata_i[0] == tdata_j[0]:
             return 0.0
-        corr_vals = compute_correlation(tdata_i[1], tdata_j[1])
-        corr = corr_vals[0]
-        if (1 - corr) < 0:
-            return 0.0
-        return 1 - corr
+        return 1 - compute_correlation(tdata_i[1], tdata_j[1])[0]
 
     def __cluster(tdata_i):
         return tuple(
@@ -168,7 +99,9 @@ def get_loci_names(
         __get_trait_loci, [v[1] for v in organised.items()], {})
     return tuple(loci_dict[_chr] for _chr in chromosome_names)
 
-def build_heatmap(traits_names, conn: Any):
+def build_heatmap(
+        traits_names: Sequence[str], conn: Any,
+        vertical: bool = False) -> go.Figure:
     """
     heatmap function
 
@@ -220,17 +153,21 @@ def build_heatmap(traits_names, conn: Any):
         zip(traits_ids,
             [traits[idx]["trait_fullname"] for idx in traits_order]))
 
-    return generate_clustered_heatmap(
+    return clustered_heatmap(
         process_traits_data_for_heatmap(
             organised, traits_ids, chromosome_names),
         clustered,
-        "single_heatmap_{}".format(random_string(10)),
-        y_axis=tuple(
-            ordered_traits_names[traits_ids[order]]
-            for order in traits_order),
-        y_label="Traits",
-        x_axis=chromosome_names,
-        x_label="Chromosomes",
+        x_axis={
+            "label": "Chromosomes",
+            "data": chromosome_names
+        },
+        y_axis={
+            "label": "Traits",
+            "data": tuple(
+                ordered_traits_names[traits_ids[order]]
+                for order in traits_order)
+        },
+        vertical=vertical,
         loci_names=get_loci_names(organised, chromosome_names))
 
 def compute_traits_order(slink_data, neworder: tuple = tuple()):
@@ -349,68 +286,81 @@ def process_traits_data_for_heatmap(data, trait_names, chromosome_names):
         for chr_name in chromosome_names]
     return hdata
 
-def generate_clustered_heatmap(
-        data, clustering_data, image_filename_prefix, x_axis=None,
-        x_label: str = "", y_axis=None, y_label: str = "",
+def clustered_heatmap(
+        data: Sequence[Sequence[float]], clustering_data: Sequence[float],
+        x_axis,#: Dict[Union[str, int], Union[str, Sequence[str]]],
+        y_axis: Dict[str, Union[str, Sequence[str]]],
         loci_names: Sequence[Sequence[str]] = tuple(),
-        output_dir: str = TMPDIR,
-        colorscale=((0.0, '#0000FF'), (0.5, '#00FF00'), (1.0, '#FF0000'))):
+        vertical: bool = False,
+        colorscale: Sequence[Sequence[Union[float, str]]] = (
+            (0.0, '#0000FF'), (0.5, '#00FF00'), (1.0, '#FF0000'))) -> go.Figure:
     """
     Generate a dendrogram, and heatmaps for each chromosome, and put them all
     into one plot.
     """
     # pylint: disable=[R0913, R0914]
-    num_cols = 1 + len(x_axis)
+    x_axis_data = x_axis["data"]
+    y_axis_data = y_axis["data"]
+    num_plots = 1 + len(x_axis_data)
     fig = make_subplots(
-        rows=1,
-        cols=num_cols,
-        shared_yaxes="rows",
+        rows=num_plots if vertical else 1,
+        cols=1 if vertical else num_plots,
+        shared_xaxes="columns" if vertical else False,
+        shared_yaxes=False if vertical else "rows",
+        vertical_spacing=0.010,
         horizontal_spacing=0.001,
-        subplot_titles=["distance"] + x_axis,
+        subplot_titles=["" if vertical else x_axis["label"]] + [
+            "Chromosome: {}".format(chromo) if vertical else chromo
+            for chromo in x_axis_data],#+ x_axis_data,
         figure=ff.create_dendrogram(
-            np.array(clustering_data), orientation="right", labels=y_axis))
+            np.array(clustering_data),
+            orientation="bottom" if vertical else "right",
+            labels=y_axis_data))
     hms = [go.Heatmap(
         name=chromo,
-        x=loci,
-        y=y_axis,
+        x=y_axis_data if vertical else loci,
+        y=loci if vertical else y_axis_data,
         z=data_array,
+        transpose=vertical,
         showscale=False)
            for chromo, data_array, loci
-           in zip(x_axis, data, loci_names)]
+           in zip(x_axis_data, data, loci_names)]
     for i, heatmap in enumerate(hms):
-        fig.add_trace(heatmap, row=1, col=(i + 2))
-
-    fig.update_layout(
-        {
-            "width": 1500,
-            "height": 800,
-            "xaxis": {
+        fig.add_trace(
+            heatmap,
+            row=((i + 2) if vertical else 1),
+            col=(1 if vertical else (i + 2)))
+
+    axes_layouts = {
+        "{axis}axis{count}".format(
+            axis=("y" if vertical else "x"),
+            count=(i+1 if i > 0 else "")): {
                 "mirror": False,
-                "showgrid": True,
-                "title": x_label
-            },
-            "yaxis": {
-                "title": y_label
+                "showticklabels": i == 0,
+                "ticks": "outside" if i == 0 else ""
             }
-        })
+        for i in range(num_plots)}
 
-    x_axes_layouts = {
-        "xaxis{}".format(i+1 if i > 0 else ""): {
-            "mirror": False,
-            "showticklabels": i == 0,
-            "ticks": "outside" if i == 0 else ""
-        }
-        for i in range(num_cols)}
+    print("vertical?: {} ==> {}".format("T" if vertical else "F", axes_layouts))
 
-    fig.update_layout(
-        {
-            "width": 4000,
-            "height": 800,
-            "yaxis": {
-                "mirror": False,
-                "ticks": ""
-            },
-            **x_axes_layouts})
+    fig.update_layout({
+        "width": 800 if vertical else 4000,
+        "height": 4000 if vertical else 800,
+        "{}axis".format("x" if vertical else "y"): {
+            "mirror": False,
+            "ticks": "",
+            "side": "top" if vertical else "left",
+            "title": y_axis["label"],
+            "tickangle": 90 if vertical else 0,
+            "ticklabelposition": "outside top" if vertical else "outside left"
+        },
+        "{}axis".format("y" if vertical else "x"): {
+            "mirror": False,
+            "showgrid": True,
+            "title": "Distance",
+            "side": "right" if vertical else "top"
+        },
+        **axes_layouts})
     fig.update_traces(
         showlegend=False,
         colorscale=colorscale,
@@ -418,7 +368,5 @@ def generate_clustered_heatmap(
     fig.update_traces(
         showlegend=True,
         showscale=True,
-        selector={"name": x_axis[-1]})
-    image_filename = "{}/{}.html".format(output_dir, image_filename_prefix)
-    fig.write_html(image_filename)
-    return image_filename, fig
+        selector={"name": x_axis_data[-1]})
+    return fig
diff --git a/gn3/settings.py b/gn3/settings.py
index 150d96d..0ac6698 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -17,14 +17,10 @@ RQTL_WRAPPER = "rqtl_wrapper.R"
 SQL_URI = os.environ.get(
     "SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl")
 SECRET_KEY = "password"
-SQLALCHEMY_TRACK_MODIFICATIONS = False
 # gn2 results only used in fetching dataset info
 
 GN2_BASE_URL = "http://www.genenetwork.org/"
 
-# biweight script
-BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R"
-
 # wgcna script
 WGCNA_RSCRIPT = "wgcna_analysis.R"
 # qtlreaper command
@@ -35,13 +31,26 @@ GENOTYPE_FILES = os.environ.get(
     "GENOTYPE_FILES", "{}/genotype_files/genotype".format(os.environ.get("HOME")))
 
 # CROSS-ORIGIN SETUP
-CORS_ORIGINS = [
+def parse_env_cors(default):
+    """Parse comma-separated configuration into list of strings."""
+    origins_str = os.environ.get("CORS_ORIGINS", None)
+    if origins_str:
+        return [
+            origin.strip() for origin in origins_str.split(",") if origin != ""]
+    return default
+
+CORS_ORIGINS = parse_env_cors([
     "http://localhost:*",
     "http://127.0.0.1:*"
-]
+])
 
 CORS_HEADERS = [
     "Content-Type",
     "Authorization",
     "Access-Control-Allow-Credentials"
 ]
+
+GNSHARE = os.environ.get("GNSHARE", "/gnshare/gn/")
+TEXTDIR = f"{GNSHARE}/web/ProbeSetFreeze_DataMatrix"
+
+ROUND_TO = 10
diff --git a/guix.scm b/guix.scm
index 9b8f399..9bf23c8 100644
--- a/guix.scm
+++ b/guix.scm
@@ -17,72 +17,47 @@
 ;;; You should have received a copy of the GNU General Public License
 ;;; along with genenetwork3. If not, see https://www.gnu.org/licenses/.
 
-;; To use this file to build HEAD of gemma:
-;;
-;;   env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix build -f guix.scm
-;;
-;; After checking out the git repo
-;;   cd ~ ; git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
+;; Make sure you have the
+;; https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics channel
+;; set up.
 ;;
 ;; To get a development container (e.g., run in emacs shell).
 ;;
-;;   env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix environment -C -l guix.scm
+;;   guix shell -C -Df guix.scm
 
-(use-modules
- (srfi srfi-1)
- (srfi srfi-26)
- (ice-9 match)
- (ice-9 popen)
- (ice-9 rdelim)
- (gn packages gemma)
- (gn packages python)
- (gnu packages base)
- (gnu packages check)
- (gnu packages graph)
- (gnu packages cran)
- (gnu packages databases)
- (gnu packages statistics)
- (gnu packages bioconductor)
- (gnu packages golang)
- (gn packages genenetwork)
- (gnu packages python)
- (gnu packages python-check)
- (gnu packages python-crypto)
- (gnu packages python-web)
- (gnu packages python-xyz)
- (gnu packages python-science)
- ((guix build utils) #:select (with-directory-excursion))
- (guix build-system python)
- (guix gexp)
- (guix git-download)
- (guix licenses)
- (guix packages))
+(use-modules (gn packages gemma)
+             (gn packages python)
+             (gnu packages base)
+             (gnu packages check)
+             (gnu packages graph)
+             (gnu packages cran)
+             (gnu packages databases)
+             (gnu packages statistics)
+             (gnu packages bioconductor)
+             (gnu packages golang)
+             (gn packages genenetwork)
+             (gnu packages python)
+             (gnu packages python-check)
+             (gnu packages python-crypto)
+             (gnu packages python-web)
+             (gnu packages python-xyz)
+             (gnu packages python-science)
+             ((guix build utils) #:select (with-directory-excursion))
+             (guix build-system python)
+             (guix gexp)
+             (guix git-download)
+             (guix licenses)
+             (guix packages))
 
 (define %source-dir (dirname (current-filename)))
 
-(define git-file?
-  (let* ((pipe (with-directory-excursion %source-dir
-                 (open-pipe* OPEN_READ "git" "ls-files")))
-         (files (let loop ((lines '()))
-                  (match (read-line pipe)
-                    ((? eof-object?)
-                     (reverse lines))
-                    (line
-                     (loop (cons line lines))))))
-         (status (close-pipe pipe)))
-    (lambda (file stat)
-      (match (stat:type stat)
-        ('directory #t)
-        ((or 'regular 'symlink)
-         (any (cut string-suffix? <> file) files))
-        (_ #f)))))
 
 (package
   (name "genenetwork3.git")
-  (version "0.0.1")
-  (source (local-file %source-dir
+  (version "0.1.0")
+  (source (local-file %source-dir "genenetwork3-checkout"
                       #:recursive? #t
-                      #:select? git-file?))
+                      #:select? (git-predicate %source-dir)))
   (propagated-inputs `(("coreutils" ,coreutils)
                        ("gemma-wrapper" ,gemma-wrapper)
                        ("gunicorn" ,gunicorn)
@@ -90,27 +65,25 @@
                        ("python-bcrypt" ,python-bcrypt)
                        ("python-flask" ,python-flask)
                        ("python-flask-cors" ,python-flask-cors)
+                       ("python-flask-socketio" ,python-flask-socketio)
                        ("python-ipfshttpclient" ,python-ipfshttpclient)
                        ("python-mypy" ,python-mypy)
                        ("python-mypy-extensions" ,python-mypy-extensions)
                        ("python-mysqlclient" ,python-mysqlclient)
                        ("python-numpy" ,python-numpy)
+                       ("python-pandas" ,python-pandas)
+                       ("python-pingouin" ,python-pingouin)
                        ("python-plotly" ,python-plotly)
                        ("python-pylint" ,python-pylint)
                        ("python-redis" ,python-redis)
                        ("python-requests" ,python-requests)
                        ("python-scipy" ,python-scipy)
-                       ("python-sqlalchemy-stubs"
-                        ,python-sqlalchemy-stubs)
                        ("r-optparse" ,r-optparse)
                        ("r-qtl" ,r-qtl)
+                       ("r-rjson" ,r-rjson)
                        ("r-stringi" ,r-stringi)
                        ("r-wgcna" ,r-wgcna)
-                       ("r-rjson" ,r-rjson)
-                       ("python-plotly" ,python-plotly)
-                       ("python-pandas" ,python-pandas)
-                       ("rust-qtlreaper" ,rust-qtlreaper)
-                       ("python-flask-cors" ,python-flask-cors)))
+                       ("rust-qtlreaper" ,rust-qtlreaper)))
   (build-system python-build-system)
   (home-page "https://github.com/genenetwork/genenetwork3")
   (synopsis "GeneNetwork3 API for data science and machine learning.")
diff --git a/mypy.ini b/mypy.ini
index 5d66812..b0c48df 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -11,3 +11,12 @@ ignore_missing_imports = True
 
 [mypy-ipfshttpclient.*]
 ignore_missing_imports = True
+
+[mypy-pingouin.*]
+ignore_missing_imports = True
+
+[mypy-redis.*]
+ignore_missing_imports = True
+
+[mypy-requests.*]
+ignore_missing_imports = True
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index d332a96..e268674 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -35,3 +35,4 @@ Werkzeug==1.0.1
 wrapt==1.12.1
 plotly==4.14.3
 flask-cors==3.0.9
+pingouin
diff --git a/scripts/calculate_biweight.R b/scripts/calculate_biweight.R
deleted file mode 100644
index 8d8366e..0000000
--- a/scripts/calculate_biweight.R
+++ /dev/null
@@ -1,43 +0,0 @@
-
-library(testthat)
-library(WGCNA)
-
-arg_values <- commandArgs(trailingOnly = TRUE)
-ParseArgs <- function(args){
-
-    trait_vals <- as.numeric(unlist(strsplit(args[1], split=" ")))
-    target_vals <- as.numeric(unlist(strsplit(args[2], split=" ")))
-
-    return(list(trait_vals= c(trait_vals),target_vals = c(target_vals)))
-
-}
-BiweightMidCorrelation <- function(trait_val,target_val){
-
-    results <-bicorAndPvalue(as.numeric(unlist(trait_val)),as.numeric(unlist(target_val)))
-    return ((c(c(results$bicor)[1],c(results$p)[1])))
-
-}
-
-
-
-test_that("biweight results"),{
-    vec_1 <- c(1,2,3,4)
-    vec_2 <- c(1,2,3,4)
-
-    results <- BiweightMidCorrelation(vec_1,vec_2)
-    expect_equal(c(1.0,0.0),results)
-}
-
-
-test_that("parsing args "),{
-    my_args <- c("1 2 3 4","5 6 7 8")
-    results <- ParseArgs(my_args)
-
-    expect_equal(results[1],c(1,2,3,4))
-    expect_equal(results[2],c(5,6,7,8))
-}
-
-parsed_values <- ParseArgs(arg_values)
-
-
-cat(BiweightMidCorrelation(parsed_values[1],parsed_values[2]))
\ No newline at end of file
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 17b3537..b0d25a9 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -6,11 +6,13 @@ library(rjson)
 
 options(stringsAsFactors = FALSE);
 
-imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
+cat("Running the wgcna analysis script\n")
+
 # load expression data **assumes from json files row(traits)(columns info+samples)
 # pass the file_path as arg
 # pass the file path to read json data
 
+
 args = commandArgs(trailingOnly=TRUE)
 
 if (length(args)==0) {
@@ -21,6 +23,7 @@ if (length(args)==0) {
 }
 
 inputData <- fromJSON(file = json_file_path)
+imgDir = inputData$TMPDIR
 
 
 trait_sample_data <- do.call(rbind, inputData$trait_sample_data)
@@ -83,6 +86,11 @@ network <- blockwiseModules(dataExpr,
 
 
 
+cat("Generated network \n")
+
+network
+
+
 genImageRandStr <- function(prefix){
 
 	randStr <- paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
@@ -90,14 +98,19 @@ genImageRandStr <- function(prefix){
 	return(paste(randStr,".png",sep=""))
 }
 
+
 mergedColors <- labels2colors(network$colors)
 
 imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
 png(imageLoc,width=1000,height=600,type='cairo-png')
 
+
+cat("Generating the CLuster  dendrogram\n")
+
+
 plotDendroAndColors(network$dendrograms[[1]],mergedColors[network$blockGenes[[1]]],
 "Module colors",
-dendroLabels = FALSE, hang = 0.03,
+dendroLabels = NULL, hang = 0.03,
 addGuide = TRUE, guideHang = 0.05)
 
 
diff --git a/setup.py b/setup.py
index 98a076f..55b4be2 100644
--- a/setup.py
+++ b/setup.py
@@ -19,7 +19,6 @@ setup(author='Bonface M. K.',
           "redis==3.5.3"
           "requests==2.25.1"
           "scipy==1.6.0"
-          "sqlalchemy-stubs==0.4"
           "plotly==4.14.3"
           "flask-cors==3.0.9"
       ],
diff --git a/sql/update/json_diff_update.sql b/sql/update/json_diff_update.sql
new file mode 100644
index 0000000..e18b285
--- /dev/null
+++ b/sql/update/json_diff_update.sql
@@ -0,0 +1,22 @@
+-- metadata_audit.sql ---
+
+-- Copyright (C) 2021 Bonface Munyoki K. <me@bonfacemunyoki.com>
+
+-- Author: Bonface Munyoki K. <me@bonfacemunyoki.com>
+
+-- This program is free software; you can redistribute it and/or
+-- modify it under the terms of the GNU 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 General Public License for more details.
+
+-- You should have received a copy of the GNU General Public License
+-- along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+-- Update the json_diff_data column to TEXT
+ALTER TABLE metadata_audit
+MODIFY json_diff_data TEXT NOT NULL;
diff --git a/tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv b/tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv
new file mode 100644
index 0000000..a1558a0
--- /dev/null
+++ b/tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv
@@ -0,0 +1,101 @@
+"function_name","count","x","y","z","method","rm","result"
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+"pcor.mat",14,"-4.90339081734419, 72.9479049798101, 46.9192364253104, 92.628131667152, 56.5425228327513, 9.90580045618117, -61.4272825885564, 33.6759516969323, 81.8828757386655, 77.3399218916893, 67.7938031964004, 94.0767949912697, 82.1635375730693, -75.240781577304","21.4586552698165, -36.5642888005823, -38.3646843954921, -49.740192014724, -81.6746165510267, -19.1730958875269, 41.690668836236, -23.3391010668129, -78.1760632060468, 77.431286778301, 70.3289750963449, 39.766847435385, 3.62148815765977, 10.747673548758","17.7063988521695, 90.0697568897158, -93.0447159335017, 85.4728828649968, -18.4118247125298, -9.85785778611898, 70.2666643075645, -97.7391937281936, 54.3527046684176, -51.4394805766642, 39.0205434523523, -25.6685835774988, -14.7992834448814, 81.1236747074872","p",FALSE,-0.21445656018345
+"pcor.mat",15,"-76.8736738711596, -35.8509941026568, -48.1256343889982, -9.57123078405857, -72.2122399602085, -6.98926709592342, -31.3491718843579, 74.3320995010436, 54.9155391287059, -46.5018933173269, 51.3019453268498, 17.0857016462833, -99.9900157097727, -17.3139852005988, -85.5749220587313","-97.7581001352519, -97.2672377247363, -27.3427923209965, -1.21665806509554, -8.05344670079648, 21.0991605184972, -54.0536799002439, 95.0312656350434, 23.7382718361914, -98.728937190026, -80.2528636530042, -59.6354123670608, 20.57563085109, 90.7686199061573, 19.6493336930871","-38.4617018979043, 28.0117013957351, -74.6210919693112, -34.3639187980443, -28.0167740304023, -46.0126685444266, 37.4354778788984, 41.0279822535813, 80.8140107430518, -94.7356107644737, -91.9223290402442, -34.4586562830955, 90.2129443362355, 76.8807396292686, 80.0070276483893","k",FALSE,0.250746493151452
+"pcor.mat",7,"-66.7350410018116, 53.2712059561163, -43.8059563748538, -44.9987557251006, -67.2016165219247, 17.9846523795277, 77.0553316920996","-60.9613332431763, 99.9187499284744, -27.7070741169155, 14.3416102975607, -30.3307291120291, 5.47642167657614, -52.1709493827075","5.97298364154994, 70.3716231975704, -16.247583553195, 92.1821707859635, -80.4653100203723, -7.83197041600943, -66.9684283901006","k",TRUE,0.241209075662211
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+"pcor.mat",8,"70.9466312080622, -31.7683406174183, 25.0176505185664, -56.8918467033654, -9.20995227061212, 84.6444204915315, 66.9992076698691, -14.915213920176","-25.2351951319724, 53.1852985266596, 32.9547242727131, -82.4257594533265, -51.8481220584363, 61.490266257897, 16.8974718544632, -71.770367724821","25.6255140993744, 62.6514744479209, 2.26075490936637, -90.3473023790866, -8.56978320516646, 89.0561478678137, 3.07730589993298, 45.6199106760323","p",FALSE,0.307942034203085
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diff --git a/tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv b/tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv
new file mode 100644
index 0000000..a1558a0
--- /dev/null
+++ b/tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv
@@ -0,0 +1,101 @@
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diff --git a/tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt b/tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt
new file mode 100644
index 0000000..6254902
--- /dev/null
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+input.z.3: -73.5004779882729, 87.9872216377407, 92.7410830743611, -13.9436025172472, 64.5655245985836, -42.4590483307838, 36.8305039592087, -82.2956138756126, -6.28325091674924, -18.8072303775698, -80.3971918765455, -1.98830938898027, 35.4344930965453, -68.9127727877349, 34.085252834484, 42.8761828225106, -8.14059982076287
+------------------------------------------------------------
+function_name: pcor.rec
+count: 12
+x: 22.8633187245578, 98.9057261962444, 24.6264463290572, -67.5152567680925, -14.0114265028387, -23.4609092120081, -16.0529976245016, -74.1293652914464, -38.613182771951, 21.516504464671, -63.1570098455995, 3.43058109283447
+y: 66.3851822260767, 15.0869043543935, 34.2552722897381, -47.5028248038143, -18.82304972969, 7.55783263593912, 87.5256262719631, -45.0442485976964, 22.7592587005347, 15.5071972869337, 6.64250506088138, -61.0094598028809
+method: k
+rm: FALSE
+result: 0.380642612922639
+input.z.1: -43.5355789028108, 3.15432427451015, 42.3869500402361, -85.9040122944862, -91.3019767962396, -4.38300650566816, -36.0976214520633, 82.1006664074957, -86.6311294957995, -17.1651322394609, 45.6184559967369, 78.0932303052396
+input.z.2: -50.4019991960377, 53.8435474969447, 46.2169490288943, 57.7160312794149, -80.6737503968179, 4.29811356589198, -8.02055508829653, -29.807900544256, -26.4149129390717, 54.7383895143867, -1.05271721258759, 2.92500704526901
+input.z.3: 82.1892600506544, 1.68216228485107, -81.9020131602883, 21.994966128841, -25.5232597701252, 56.1190348584205, -62.1999088674784, -84.2725639231503, -35.7946417294443, -20.4277000855654, -81.0949407052249, 48.0415523983538
+------------------------------------------------------------
diff --git a/tests/unit/computations/test_biweight.py b/tests/unit/computations/test_biweight.py
deleted file mode 100644
index ad404f1..0000000
--- a/tests/unit/computations/test_biweight.py
+++ /dev/null
@@ -1,21 +0,0 @@
-"""test for biweight script"""
-from unittest import TestCase
-from unittest import mock
-
-from gn3.computations.biweight import calculate_biweight_corr
-
-
-class TestBiweight(TestCase):
-    """test class for biweight"""
-
-    @mock.patch("gn3.computations.biweight.subprocess.check_output")
-    def test_calculate_biweight_corr(self, mock_check_output):
-        """test for calculate_biweight_corr func"""
-        mock_check_output.return_value = "0.1 0.5"
-        results = calculate_biweight_corr(command="Rscript",
-                                          path_to_script="./r_script.R",
-                                          trait_vals=[
-                                              1.2, 1.1, 1.9],
-                                          target_vals=[1.9, 0.4, 1.1])
-
-        self.assertEqual(results, (0.1, 0.5))
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index fc52ec1..d60dd62 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -1,14 +1,17 @@
 """Module contains the tests for correlation"""
 from unittest import TestCase
 from unittest import mock
+import unittest
 
 from collections import namedtuple
+import math
+from numpy.testing import assert_almost_equal
 
 from gn3.computations.correlations import normalize_values
-from gn3.computations.correlations import do_bicor
 from gn3.computations.correlations import compute_sample_r_correlation
 from gn3.computations.correlations import compute_all_sample_correlation
 from gn3.computations.correlations import filter_shared_sample_keys
+
 from gn3.computations.correlations import tissue_correlation_for_trait
 from gn3.computations.correlations import lit_correlation_for_trait
 from gn3.computations.correlations import fetch_lit_correlation_data
@@ -94,20 +97,11 @@ class TestCorrelation(TestCase):
         results = normalize_values([2.3, None, None, 3.2, 4.1, 5],
                                    [3.4, 7.2, 1.3, None, 6.2, 4.1])
 
-        expected_results = ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
-
-        self.assertEqual(results, expected_results)
-
-    @mock.patch("gn3.computations.correlations.calculate_biweight_corr")
-    def test_bicor(self, mock_biweight):
-        """Test for doing biweight mid correlation """
-        mock_biweight.return_value = (1.0, 0.0)
-
-        results = do_bicor(x_val=[1, 2, 3], y_val=[4, 5, 6])
+        expected_results = [(2.3, 4.1, 5), (3.4, 6.2, 4.1)]
 
-        self.assertEqual(results, (1.0, 0.0)
-                         )
+        self.assertEqual(list(zip(*list(results))), expected_results)
 
+    @unittest.skip("reason for skipping")
     @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value")
     @mock.patch("gn3.computations.correlations.normalize_values")
     def test_compute_sample_r_correlation(self, norm_vals, compute_corr):
@@ -163,22 +157,23 @@ class TestCorrelation(TestCase):
 
         }
 
-        filtered_target_samplelist = ["1.23", "6.565", "6.456"]
-        filtered_this_samplelist = ["6.266", "6.565", "6.456"]
+        filtered_target_samplelist = ("1.23", "6.565", "6.456")
+        filtered_this_samplelist = ("6.266", "6.565", "6.456")
 
         results = filter_shared_sample_keys(
             this_samplelist=this_samplelist, target_samplelist=target_samplelist)
 
-        self.assertEqual(results, (filtered_this_samplelist,
-                                   filtered_target_samplelist))
+        self.assertEqual(list(zip(*list(results))), [filtered_this_samplelist,
+                                                     filtered_target_samplelist])
 
     @mock.patch("gn3.computations.correlations.compute_sample_r_correlation")
     @mock.patch("gn3.computations.correlations.filter_shared_sample_keys")
     def test_compute_all_sample(self, filter_shared_samples, sample_r_corr):
         """Given target dataset compute all sample r correlation"""
 
-        filter_shared_samples.return_value = (["1.23", "6.565", "6.456"], [
-            "6.266", "6.565", "6.456"])
+        filter_shared_samples.return_value = [iter(val) for val in [(
+            "1.23", "6.266"), ("6.565", "6.565"), ("6.456", "6.456")]]
+
         sample_r_corr.return_value = (["1419792_at", -1.0, 0.9, 6])
 
         this_trait_data = {
@@ -210,10 +205,8 @@ class TestCorrelation(TestCase):
             this_trait=this_trait_data, target_dataset=traits_dataset), sample_all_results)
         sample_r_corr.assert_called_once_with(
             trait_name='1419792_at',
-            corr_method="pearson", trait_vals=['1.23', '6.565', '6.456'],
-            target_samples_vals=['6.266', '6.565', '6.456'])
-        filter_shared_samples.assert_called_once_with(
-            this_trait_data.get("trait_sample_data"), traits_dataset[0].get("trait_sample_data"))
+            corr_method="pearson", trait_vals=('1.23', '6.565', '6.456'),
+            target_samples_vals=('6.266', '6.565', '6.456'))
 
     @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value")
     def test_tissue_correlation_for_trait(self, mock_compute_corr_coeff):
@@ -479,10 +472,10 @@ class TestCorrelation(TestCase):
                  [None, None, None, None, None, None, None, None, None, 0],
                  (0.0, 1)],
                 [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
-                 (0, 10)],
+                 (math.nan, 10)],
                 [[9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87],
                  [9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87],
-                 (0.9999999999999998, 10)],
+                 (math.nan, 10)],
                 [[9.3, 2.2, 5.4, 7.2, 6.4, 7.6, 3.8, 1.8, 8.4, 0.2],
                  [0.6, 3.97, 5.82, 8.21, 1.65, 4.55, 6.72, 9.5, 7.33, 2.34],
                  (-0.12720361919462056, 10)],
@@ -490,5 +483,8 @@ class TestCorrelation(TestCase):
                  [None, None, None, None, 2, None, None, 3, None, None],
                  (0.0, 2)]]:
             with self.subTest(dbdata=dbdata, userdata=userdata):
-                self.assertEqual(compute_correlation(
-                    dbdata, userdata), expected)
+                actual = compute_correlation(dbdata, userdata)
+                with self.subTest("correlation coefficient"):
+                    assert_almost_equal(actual[0], expected[0])
+                with self.subTest("overlap"):
+                    self.assertEqual(actual[1], expected[1])
diff --git a/tests/unit/computations/test_partial_correlations.py b/tests/unit/computations/test_partial_correlations.py
new file mode 100644
index 0000000..3690ca4
--- /dev/null
+++ b/tests/unit/computations/test_partial_correlations.py
@@ -0,0 +1,299 @@
+"""Module contains tests for gn3.partial_correlations"""
+
+from unittest import TestCase
+
+import pandas
+from numpy.testing import assert_allclose
+
+from gn3.computations.partial_correlations import (
+    fix_samples,
+    control_samples,
+    build_data_frame,
+    dictify_by_samples,
+    tissue_correlation,
+    find_identical_traits,
+    good_dataset_samples_indexes)
+
+sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
+control_traits = (
+    {
+        "mysqlid": 36688172,
+        "data": {
+            "B6cC3-1": {
+                "sample_name": "B6cC3-1", "value": 7.51879, "variance": None,
+                "ndata": None},
+            "BXD1": {
+                "sample_name": "BXD1", "value": 7.77141, "variance": None,
+                "ndata": None},
+            "BXD12": {
+                "sample_name": "BXD12", "value": 8.39265, "variance": None,
+                "ndata": None},
+            "BXD16": {
+                "sample_name": "BXD16", "value": 8.17443, "variance": None,
+                "ndata": None},
+            "BXD19": {
+                "sample_name": "BXD19", "value": 8.30401, "variance": None,
+                "ndata": None},
+            "BXD2": {
+                "sample_name": "BXD2", "value": 7.80944, "variance": None,
+                "ndata": None}}},
+    {
+        "mysqlid": 36688172,
+        "data": {
+            "B6cC3-21": {
+                "sample_name": "B6cC3-1", "value": 7.51879, "variance": None,
+                "ndata": None},
+            "BXD21": {
+                "sample_name": "BXD1", "value": 7.77141, "variance": None,
+                "ndata": None},
+            "BXD12": {
+                "sample_name": "BXD12", "value": 8.39265, "variance": None,
+                "ndata": None},
+            "BXD16": {
+                "sample_name": "BXD16", "value": 8.17443, "variance": None,
+                "ndata": None},
+            "BXD19": {
+                "sample_name": "BXD19", "value": 8.30401, "variance": None,
+                "ndata": None},
+            "BXD2": {
+                "sample_name": "BXD2", "value": 7.80944, "variance": None,
+                "ndata": None}}},
+    {
+        "mysqlid": 36688172,
+        "data": {
+            "B6cC3-1": {
+                "sample_name": "B6cC3-1", "value": 7.51879, "variance": None,
+                "ndata": None},
+            "BXD1": {
+                "sample_name": "BXD1", "value": 7.77141, "variance": None,
+                "ndata": None},
+            "BXD12": {
+                "sample_name": "BXD12", "value": None, "variance": None,
+                "ndata": None},
+            "BXD16": {
+                "sample_name": "BXD16", "value": None, "variance": None,
+                "ndata": None},
+            "BXD19": {
+                "sample_name": "BXD19", "value": None, "variance": None,
+                "ndata": None},
+            "BXD2": {
+                "sample_name": "BXD2", "value": 7.80944, "variance": None,
+                "ndata": None}}})
+
+dictified_control_samples = (
+    {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None},
+     "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None},
+     "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None},
+     "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None},
+     "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None},
+     "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}},
+    {"BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None},
+     "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None},
+     "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None},
+     "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None}},
+    {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None},
+     "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None},
+     "BXD2": {"sample_name": "BXD2", "value":  7.80944, "variance": None}})
+
+class TestPartialCorrelations(TestCase):
+    """Class for testing partial correlations computation functions"""
+
+    def test_control_samples(self):
+        """Test that the control_samples works as expected."""
+        self.assertEqual(
+            control_samples(control_traits, sampleslist),
+            ((("B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"),
+              ("BXD12", "BXD16", "BXD19", "BXD2"),
+              ("B6cC3-1", "BXD1", "BXD2")),
+             ((7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944),
+              (8.39265, 8.17443, 8.30401, 7.80944),
+              (7.51879, 7.77141, 7.80944)),
+             ((None, None, None, None, None, None), (None, None, None, None),
+              (None, None, None)),
+             (6, 4, 3)))
+
+    def test_dictify_by_samples(self):
+        """
+        Test that `dictify_by_samples` generates the appropriate dict
+
+        Given:
+            a sequence of sequences with sample names, values and variances, as
+            in the output of `gn3.partial_correlations.control_samples` or
+            the output of `gn3.db.traits.export_informative`
+        When:
+            the sequence is passed as an argument into the
+            `gn3.partial_correlations.dictify_by_sample`
+        Then:
+            return a sequence of dicts with keys being the values of the sample
+            names, and each of who's values being sub-dicts with the keys
+            'sample_name', 'value' and 'variance' whose values correspond to the
+            values passed in.
+        """
+        self.assertEqual(
+            dictify_by_samples(
+                ((("B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"),
+                  ("BXD12", "BXD16", "BXD19", "BXD2"),
+                  ("B6cC3-1", "BXD1", "BXD2")),
+                 ((7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944),
+                  (8.39265, 8.17443, 8.30401, 7.80944),
+                  (7.51879, 7.77141, 7.80944)),
+                 ((None, None, None, None, None, None), (None, None, None, None),
+                  (None, None, None)),
+                 (6, 4, 3))),
+            dictified_control_samples)
+
+    def test_fix_samples(self):
+        """
+        Test that `fix_samples` returns only the common samples
+
+        Given:
+            - A primary trait
+            - A sequence of control samples
+        When:
+            - The two arguments are passed to `fix_samples`
+        Then:
+            - Only the names of the samples present in the primary trait that
+              are also present in ALL the control traits are present in the
+              return value
+            - Only the values of the samples present in the primary trait that
+              are also present in ALL the control traits are present in the
+              return value
+            - ALL the values for ALL the control traits are present in the
+              return value
+            - Only the variances of the samples present in the primary trait
+              that are also present in ALL the control traits are present in the
+              return value
+            - ALL the variances for ALL the control traits are present in the
+              return value
+            - The return value is a tuple of the above items, in the following
+              order:
+                ((sample_names, ...), (primary_trait_values, ...),
+                 (control_traits_values, ...), (primary_trait_variances, ...)
+                 (control_traits_variances, ...))
+        """
+        self.assertEqual(
+            fix_samples(
+                {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879,
+                             "variance": None},
+                 "BXD1": {"sample_name": "BXD1", "value": 7.77141,
+                          "variance": None},
+                 "BXD2": {"sample_name": "BXD2", "value":  7.80944,
+                          "variance": None}},
+                dictified_control_samples),
+            (("BXD2",), (7.80944,),
+             (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944, 8.39265,
+              8.17443, 8.30401, 7.80944, 7.51879, 7.77141, 7.80944),
+             (None,),
+             (None, None, None, None, None, None, None, None, None, None, None,
+              None, None)))
+
+    def test_find_identical_traits(self):
+        """
+        Test `gn3.partial_correlations.find_identical_traits`.
+
+        Given:
+            - the name of a primary trait
+            - a sequence of values for the primary trait
+            - a sequence of names of control traits
+            - a sequence of values of control traits
+        When:
+            - the arguments above are passed to the `find_identical_traits`
+              function
+        Then:
+            - Return ALL trait names that have the same value when up to three
+              decimal places are considered
+        """
+        for primn, primv, contn, contv, expected in (
+                ("pt", (12.98395,), ("ct0", "ct1", "ct2"),
+                 ((0.1234, 2.3456, 3.4567),), tuple()),
+                ("pt", (12.98395, 2.3456, 3.4567), ("ct0", "ct1", "ct2"),
+                 ((12.98354, 2.3456, 3.4567), (64.2334, 6.3256, 64.2364),
+                  (4.2374, 67.2345, 7.48234)), ("pt", "ct0")),
+                ("pt", (12.98395, 75.52382), ("ct0", "ct1", "ct2", "ct3"),
+                 ((0.1234, 2.3456), (0.3621, 6543.572), (0.1234, 2.3456),
+                  (0.1233, 4.5678)), ("ct0", "ct2"))
+        ):
+            with self.subTest(
+                    primary_name=primn, primary_value=primv,
+                    control_names=contn, control_values=contv):
+                self.assertEqual(
+                    find_identical_traits(primn, primv, contn, contv), expected)
+
+    def test_tissue_correlation_error(self):
+        """
+        Test that `tissue_correlation` raises specific exceptions for particular
+        error conditions.
+        """
+        for primary, target, method, error, error_msg in (
+                ((1, 2, 3), (4, 5, 6, 7), "pearson",
+                 AssertionError,
+                 (
+                     "The lengths of the `primary_trait_values` and "
+                     "`target_trait_values` must be equal")),
+                ((1, 2, 3), (4, 5, 6, 7), "spearman",
+                 AssertionError,
+                 (
+                     "The lengths of the `primary_trait_values` and "
+                     "`target_trait_values` must be equal")),
+                ((1, 2, 3, 4), (5, 6, 7), "pearson",
+                 AssertionError,
+                 (
+                     "The lengths of the `primary_trait_values` and "
+                     "`target_trait_values` must be equal")),
+                ((1, 2, 3, 4), (5, 6, 7), "spearman",
+                 AssertionError,
+                 (
+                     "The lengths of the `primary_trait_values` and "
+                     "`target_trait_values` must be equal")),
+                ((1, 2, 3), (4, 5, 6), "nonexistentmethod",
+                 AssertionError,
+                 (
+                     "Method must be one of: pearson, spearman"))):
+            with self.subTest(primary=primary, target=target, method=method):
+                with self.assertRaises(error, msg=error_msg):
+                    tissue_correlation(primary, target, method)
+
+    def test_tissue_correlation(self): # pylint: disable=R0201
+        """
+        Test that the correct correlation values are computed for the given:
+        - primary trait
+        - target trait
+        - method
+        """
+        for primary, target, method, expected in (
+                ((12.34, 18.36, 42.51), (37.25, 46.25, 46.56), "pearson",
+                 (0.6761779252651052, 0.5272701133657985)),
+                ((1, 2, 3, 4, 5), (5, 6, 7, 8, 7), "spearman",
+                 (0.8207826816681233, 0.08858700531354381))):
+            with self.subTest(primary=primary, target=target, method=method):
+                assert_allclose(
+                    tissue_correlation(primary, target, method), expected)
+
+    def test_good_dataset_samples_indexes(self):
+        """
+        Test that `good_dataset_samples_indexes` returns correct indices.
+        """
+        self.assertEqual(
+            good_dataset_samples_indexes(
+                ("a", "e", "i", "k"),
+                ("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l")),
+            (0, 4, 8, 10))
+
+    def test_build_data_frame(self):
+        """
+        Check that the function builds the correct data frame.
+        """
+        for xdata, ydata, zdata, expected in (
+                ((0.1, 1.1, 2.1), (2.1, 3.1, 4.1), (5.1, 6.1, 7.1),
+                 pandas.DataFrame({
+                     "x": (0.1, 1.1, 2.1), "y": (2.1, 3.1, 4.1),
+                     "z": (5.1, 6.1, 7.1)})),
+                ((0.1, 1.1, 2.1), (2.1, 3.1, 4.1),
+                 ((5.1, 6.1, 7.1), (5.2, 6.2, 7.2), (5.3, 6.3, 7.3)),
+                 pandas.DataFrame({
+                     "x": (0.1, 1.1, 2.1), "y": (2.1, 3.1, 4.1),
+                     "z0": (5.1, 6.1, 7.1), "z1": (5.2, 6.2, 7.2),
+                     "z2": (5.3, 6.3, 7.3)}))):
+            with self.subTest(xdata=xdata, ydata=ydata, zdata=zdata):
+                self.assertTrue(
+                    build_data_frame(xdata, ydata, zdata).equals(expected))
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index ec81d94..5f23a86 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -10,13 +10,16 @@ from gn3.computations.wgcna import call_wgcna_script
 class TestWgcna(TestCase):
     """test class for wgcna"""
 
+    @mock.patch("gn3.computations.wgcna.process_image")
     @mock.patch("gn3.computations.wgcna.run_cmd")
     @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
     @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
     def test_call_wgcna_script(self,
                                mock_dumping_data,
                                mock_compose_wgcna,
-                               mock_run_cmd):
+                               mock_run_cmd,
+                               mock_img,
+                               ):
         """test for calling wgcna script"""
 
         # pylint: disable = line-too-long
@@ -50,7 +53,7 @@ class TestWgcna(TestCase):
             "output": "Flagging genes and samples with too many missing values...\n  ..step 1\nAllowing parallel execution with up to 3 working processes.\npickSoftThreshold: will use block size 7.\n pickSoftThreshold: calculating connectivity for given powers...\n   ..working on genes 1 through 7 of 7\n   Flagging genes and samples with too many missing values...\n    ..step 1\n ..Working on block 1 .\n    TOM calculation: adjacency..\n    ..will not use multithreading.\nclustering..\n ....detecting modules..\n ....calculating module eigengenes..\n ....checking kME in modules..\n ..merging modules that are too close..\n     mergeCloseModules: Merging modules whose distance is less than 0.15\n     mergeCloseModules: less than two proper modules.\n      ..color levels are turquoise\n      ..there is nothing to merge.\n       Calculating new MEs...\n"
         }
 
-        json_output = "{\"inputdata\":{\"trait_sample_data \":{},\"minModuleSize\":30,\"TOMtype\":\"unsigned\"},\"outputdata\":{\"eigengenes\":[],\"colors\":[]}}"
+        json_output = "{\"inputdata\":{\"trait_sample_data \":{},\"minModuleSize\":30,\"TOMtype\":\"unsigned\"},\"output\":{\"eigengenes\":[],\"imageLoc\":[],\"colors\":[]}}"
 
         expected_output = {
 
@@ -61,9 +64,11 @@ class TestWgcna(TestCase):
                     "TOMtype": "unsigned"
                 },
 
-                "outputdata": {
+                "output": {
                     "eigengenes": [],
-                    "colors": []
+                    "imageLoc": [],
+                    "colors": [],
+                    "image_data": "AFDSFNBSDGJJHH"
                 }
             },
 
@@ -74,6 +79,7 @@ class TestWgcna(TestCase):
         with mock.patch("builtins.open", mock.mock_open(read_data=json_output)):
 
             mock_run_cmd.return_value = mock_run_cmd_results
+            mock_img.return_value = b"AFDSFNBSDGJJHH"
 
             results = call_wgcna_script(
                 "Rscript/GUIX_PATH/scripts/r_file.R", request_data)
diff --git a/tests/unit/db/test_correlation.py b/tests/unit/db/test_correlation.py
new file mode 100644
index 0000000..3f940b2
--- /dev/null
+++ b/tests/unit/db/test_correlation.py
@@ -0,0 +1,96 @@
+"""
+Tests for the gn3.db.correlations module
+"""
+
+from unittest import TestCase
+
+from gn3.db.correlations import (
+    build_query_sgo_lit_corr,
+    build_query_tissue_corr)
+
+class TestCorrelation(TestCase):
+    """Test cases for correlation data fetching functions"""
+    maxDiff = None
+
+    def test_build_query_sgo_lit_corr(self):
+        """
+        Test that the literature correlation query is built correctly.
+        """
+        self.assertEqual(
+            build_query_sgo_lit_corr(
+                "Probeset",
+                "temp_table_xy45i7wd",
+                "T1.value, T2.value, T3.value",
+                (("LEFT JOIN ProbesetData AS T1 "
+                  "ON T1.Id = ProbesetXRef.DataId "
+                  "AND T1.StrainId=%(T1_sample_id)s"),
+                 (
+                     "LEFT JOIN ProbesetData AS T2 "
+                     "ON T2.Id = ProbesetXRef.DataId "
+                     "AND T2.StrainId=%(T2_sample_id)s"),
+                 (
+                     "LEFT JOIN ProbesetData AS T3 "
+                     "ON T3.Id = ProbesetXRef.DataId "
+                     "AND T3.StrainId=%(T3_sample_id)s"))),
+            (("SELECT Probeset.Name, temp_table_xy45i7wd.value, "
+              "T1.value, T2.value, T3.value "
+              "FROM (Probeset, ProbesetXRef, ProbesetFreeze) "
+              "LEFT JOIN temp_table_xy45i7wd ON temp_table_xy45i7wd.GeneId2=ProbeSet.GeneId "
+              "LEFT JOIN ProbesetData AS T1 "
+              "ON T1.Id = ProbesetXRef.DataId "
+              "AND T1.StrainId=%(T1_sample_id)s "
+              "LEFT JOIN ProbesetData AS T2 "
+              "ON T2.Id = ProbesetXRef.DataId "
+              "AND T2.StrainId=%(T2_sample_id)s "
+              "LEFT JOIN ProbesetData AS T3 "
+              "ON T3.Id = ProbesetXRef.DataId "
+              "AND T3.StrainId=%(T3_sample_id)s "
+              "WHERE ProbeSet.GeneId IS NOT NULL "
+              "AND temp_table_xy45i7wd.value IS NOT NULL "
+              "AND ProbesetXRef.ProbesetFreezeId = ProbesetFreeze.Id "
+              "AND ProbesetFreeze.Name = %(db_name)s "
+              "AND Probeset.Id = ProbesetXRef.ProbesetId "
+              "ORDER BY Probeset.Id"),
+             2))
+
+    def test_build_query_tissue_corr(self):
+        """
+        Test that the tissue correlation query is built correctly.
+        """
+        self.assertEqual(
+            build_query_tissue_corr(
+                "Probeset",
+                "temp_table_xy45i7wd",
+                "T1.value, T2.value, T3.value",
+                (("LEFT JOIN ProbesetData AS T1 "
+                  "ON T1.Id = ProbesetXRef.DataId "
+                  "AND T1.StrainId=%(T1_sample_id)s"),
+                 (
+                     "LEFT JOIN ProbesetData AS T2 "
+                     "ON T2.Id = ProbesetXRef.DataId "
+                     "AND T2.StrainId=%(T2_sample_id)s"),
+                 (
+                     "LEFT JOIN ProbesetData AS T3 "
+                     "ON T3.Id = ProbesetXRef.DataId "
+                     "AND T3.StrainId=%(T3_sample_id)s"))),
+            (("SELECT Probeset.Name, temp_table_xy45i7wd.Correlation, "
+              "temp_table_xy45i7wd.PValue, "
+              "T1.value, T2.value, T3.value "
+              "FROM (Probeset, ProbesetXRef, ProbesetFreeze) "
+              "LEFT JOIN temp_table_xy45i7wd ON temp_table_xy45i7wd.Symbol=ProbeSet.Symbol "
+              "LEFT JOIN ProbesetData AS T1 "
+              "ON T1.Id = ProbesetXRef.DataId "
+              "AND T1.StrainId=%(T1_sample_id)s "
+              "LEFT JOIN ProbesetData AS T2 "
+              "ON T2.Id = ProbesetXRef.DataId "
+              "AND T2.StrainId=%(T2_sample_id)s "
+              "LEFT JOIN ProbesetData AS T3 "
+              "ON T3.Id = ProbesetXRef.DataId "
+              "AND T3.StrainId=%(T3_sample_id)s "
+              "WHERE ProbeSet.Symbol IS NOT NULL "
+              "AND temp_table_xy45i7wd.Correlation IS NOT NULL "
+              "AND ProbesetXRef.ProbesetFreezeId = ProbesetFreeze.Id "
+              "AND ProbesetFreeze.Name = %(db_name)s "
+              "AND Probeset.Id = ProbesetXRef.ProbesetId "
+              "ORDER BY Probeset.Id"),
+             3))
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 8af8e82..4aa9389 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -2,6 +2,8 @@
 from unittest import mock, TestCase
 from gn3.db.traits import (
     build_trait_name,
+    export_trait_data,
+    export_informative,
     set_haveinfo_field,
     update_sample_data,
     retrieve_trait_info,
@@ -12,6 +14,38 @@ from gn3.db.traits import (
     retrieve_publish_trait_info,
     retrieve_probeset_trait_info)
 
+samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
+trait_data = {
+    "mysqlid": 36688172,
+    "data": {
+        "B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
+        "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
+        "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
+        "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
+        "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
+        "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
+        "BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
+        "BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
+        "BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
+        "BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
+        "BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
+        "BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
+        "BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
+        "BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
+        "BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
+        "BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
+        "BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
+        "BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
+        "BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
+        "BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
+        "BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
+        "BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
+        "BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
+        "BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
+        "C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
+        "C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
+        "DBA/2J": {"sample_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
+
 class TestTraitsDBFunctions(TestCase):
     "Test cases for traits functions"
 
@@ -226,3 +260,145 @@ class TestTraitsDBFunctions(TestCase):
             with self.subTest(trait_info=trait_info, expected=expected):
                 self.assertEqual(
                     set_confidential_field(trait_type, trait_info), expected)
+
+    def test_export_trait_data_dtype(self):
+        """
+        Test `export_trait_data` with different values for the `dtype` keyword
+        argument
+        """
+        for dtype, expected in [
+                ["val", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+                ["var", (None, None, None, None, None, None)],
+                ["N", (None, None, None, None, None, None)],
+                ["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
+            with self.subTest(dtype=dtype):
+                self.assertEqual(
+                    export_trait_data(trait_data, samplelist, dtype=dtype),
+                    expected)
+
+    def test_export_trait_data_dtype_all_flags(self):
+        """
+        Test `export_trait_data` with different values for the `dtype` keyword
+        argument and the different flags set up
+        """
+        for dtype, vflag, nflag, expected in [
+                ["val", False, False,
+                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+                ["val", False, True,
+                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+                ["val", True, False,
+                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+                ["val", True, True,
+                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+                ["var", False, False, (None, None, None, None, None, None)],
+                ["var", False, True, (None, None, None, None, None, None)],
+                ["var", True, False, (None, None, None, None, None, None)],
+                ["var", True, True, (None, None, None, None, None, None)],
+                ["N", False, False, (None, None, None, None, None, None)],
+                ["N", False, True, (None, None, None, None, None, None)],
+                ["N", True, False, (None, None, None, None, None, None)],
+                ["N", True, True, (None, None, None, None, None, None)],
+                ["all", False, False,
+                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+                ["all", False, True,
+                 (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
+                  8.30401, None, 7.80944, None)],
+                ["all", True, False,
+                 (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
+                  8.30401, None, 7.80944, None)],
+                ["all", True, True,
+                 (7.51879, None, None, 7.77141, None, None, 8.39265, None, None,
+                  8.17443, None, None, 8.30401, None, None, 7.80944, None, None)]
+        ]:
+            with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
+                self.assertEqual(
+                    export_trait_data(
+                        trait_data, samplelist, dtype=dtype, var_exists=vflag,
+                        n_exists=nflag),
+                    expected)
+
+    def test_export_informative(self):
+        """Test that the function exports appropriate data."""
+        # pylint: disable=W0621
+        for trait_data, inc_var, expected in [
+                [{"data": {
+                    "sample1": {
+                        "sample_name": "sample1", "value": 9, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample2": {
+                        "sample_name": "sample2", "value": 8, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample3": {
+                        "sample_name": "sample3", "value": 7, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample4": {
+                        "sample_name": "sample4", "value": 6, "variance": None,
+                        "ndata": 13
+                    },
+                }}, 0, (
+                    ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6),
+                    (None, None, None, None))],
+                [{"data": {
+                    "sample1": {
+                        "sample_name": "sample1", "value": 9, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample2": {
+                        "sample_name": "sample2", "value": 8, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample3": {
+                        "sample_name": "sample3", "value": None, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample4": {
+                        "sample_name": "sample4", "value": 6, "variance": None,
+                        "ndata": 13
+                    },
+                }}, 0, (
+                    ("sample1", "sample2", "sample4"), (9, 8, 6),
+                    (None, None, None))],
+                [{"data": {
+                    "sample1": {
+                        "sample_name": "sample1", "value": 9, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample2": {
+                        "sample_name": "sample2", "value": 8, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample3": {
+                        "sample_name": "sample3", "value": 7, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample4": {
+                        "sample_name": "sample4", "value": 6, "variance": None,
+                        "ndata": 13
+                    },
+                }}, True, (tuple(), tuple(), tuple())],
+                [{"data": {
+                    "sample1": {
+                        "sample_name": "sample1", "value": 9, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample2": {
+                        "sample_name": "sample2", "value": 8, "variance": 0.657,
+                        "ndata": 13
+                    },
+                    "sample3": {
+                        "sample_name": "sample3", "value": 7, "variance": None,
+                        "ndata": 13
+                    },
+                    "sample4": {
+                        "sample_name": "sample4", "value": 6, "variance": None,
+                        "ndata": 13
+                    },
+                }}, 0, (
+                    ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6),
+                    (None, 0.657, None, None))]]:
+            with self.subTest(trait_data=trait_data):
+                self.assertEqual(
+                    export_informative(trait_data, inc_var), expected)
diff --git a/tests/unit/test_authentication.py b/tests/unit/test_authentication.py
new file mode 100644
index 0000000..061b684
--- /dev/null
+++ b/tests/unit/test_authentication.py
@@ -0,0 +1,101 @@
+"""Test cases for authentication.py"""
+import json
+import unittest
+
+from unittest import mock
+from gn3.authentication import AdminRole
+from gn3.authentication import DataRole
+from gn3.authentication import get_highest_user_access_role
+from gn3.authentication import get_user_membership
+
+
+class TestGetUserMembership(unittest.TestCase):
+    """Test cases for `get_user_membership`"""
+
+    def setUp(self):
+        conn = mock.MagicMock()
+        conn.hgetall.return_value = {
+            '7fa95d07-0e2d-4bc5-b47c-448fdc1260b2': (
+                '{"name": "editors", '
+                '"admins": ["8ad942fe-490d-453e-bd37-56f252e41604", "rand"], '
+                '"members": ["8ad942fe-490d-453e-bd37-56f252e41603", '
+                '"rand"], '
+                '"changed_timestamp": "Oct 06 2021 06:39PM", '
+                '"created_timestamp": "Oct 06 2021 06:39PM"}')}
+        self.conn = conn
+
+    def test_user_is_group_member_only(self):
+        """Test that a user is only a group member"""
+        self.assertEqual(
+            get_user_membership(
+                conn=self.conn,
+                user_id="8ad942fe-490d-453e-bd37-56f252e41603",
+                group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"),
+            {"member": True,
+             "admin": False})
+
+    def test_user_is_group_admin_only(self):
+        """Test that a user is a group admin only"""
+        self.assertEqual(
+            get_user_membership(
+                conn=self.conn,
+                user_id="8ad942fe-490d-453e-bd37-56f252e41604",
+                group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"),
+            {"member": False,
+             "admin": True})
+
+    def test_user_is_both_group_member_and_admin(self):
+        """Test that a user is both an admin and member of a group"""
+        self.assertEqual(
+            get_user_membership(
+                conn=self.conn,
+                user_id="rand",
+                group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"),
+            {"member": True,
+             "admin": True})
+
+
+class TestCheckUserAccessRole(unittest.TestCase):
+    """Test cases for `get_highest_user_access_role`"""
+
+    @mock.patch("gn3.authentication.requests.get")
+    def test_edit_access(self, requests_mock):
+        """Test that the right access roles are set if the user has edit access"""
+        response = mock.PropertyMock(return_value=json.dumps(
+            {
+                'data': ['no-access', 'view', 'edit', ],
+                'metadata': ['no-access', 'view', 'edit', ],
+                'admin': ['not-admin', 'edit-access', ],
+            }
+        ))
+        type(requests_mock.return_value).content = response
+        self.assertEqual(
+            get_highest_user_access_role(
+                resource_id="0196d92e1665091f202f",
+                user_id="8ad942fe-490d-453e-bd37"),
+            {
+                "data": DataRole.EDIT,
+                "metadata": DataRole.EDIT,
+                "admin": AdminRole.EDIT_ACCESS,
+            })
+
+    @mock.patch("gn3.authentication.requests.get")
+    def test_no_access(self, requests_mock):
+        """Test that the right access roles are set if the user has no access"""
+        response = mock.PropertyMock(return_value=json.dumps(
+            {
+                'data': ['no-access', ],
+                'metadata': ['no-access', ],
+                'admin': ['not-admin', ],
+            }
+        ))
+        type(requests_mock.return_value).content = response
+        self.assertEqual(
+            get_highest_user_access_role(
+                resource_id="0196d92e1665091f202f",
+                user_id=""),
+            {
+                "data": DataRole.NO_ACCESS,
+                "metadata": DataRole.NO_ACCESS,
+                "admin": AdminRole.NOT_ADMIN,
+            })
diff --git a/tests/unit/test_data_helpers.py b/tests/unit/test_data_helpers.py
new file mode 100644
index 0000000..88ea469
--- /dev/null
+++ b/tests/unit/test_data_helpers.py
@@ -0,0 +1,89 @@
+"""
+Test functions in gn3.data_helpers
+"""
+
+from unittest import TestCase
+
+from gn3.data_helpers import partition_by, partition_all, parse_csv_line
+
+class TestDataHelpers(TestCase):
+    """
+    Test functions in gn3.data_helpers
+    """
+
+    def test_partition_all(self):
+        """
+        Test that `gn3.data_helpers.partition_all` partitions sequences as expected.
+
+        Given:
+            - `num`: The number of items per partition
+            - `items`: A sequence of items
+        When:
+            - The arguments above are passed to the `gn3.data_helpers.partition_all`
+        Then:
+            - Return a new sequence with partitions, each of which has `num`
+              items in the same order as those in `items`, save for the last
+              partition which might have fewer items than `num`.
+        """
+        for count, items, expected in (
+                (1, [0, 1, 2, 3], ((0,), (1,), (2,), (3,))),
+                (3, (0, 1, 2, 3, 4, 5, 6, 7, 8, 9),
+                 ((0, 1, 2), (3, 4, 5), (6, 7, 8), (9, ))),
+                (4, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+                 ((0, 1, 2, 3), (4, 5, 6, 7), (8, 9))),
+                (13, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+                 ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9), ))):
+            with self.subTest(n=count, items=items):
+                self.assertEqual(partition_all(count, items), expected)
+
+    def test_parse_csv_line(self):
+        """
+        Test parsing a single line from a CSV file
+
+        Given:
+            - `line`: a line read from a csv file
+            - `delimiter`: the expected delimiter in the csv file
+            - `quoting`: the quoting enclosing each column in the csv file
+        When:
+            - `line` is parsed with the `parse_csv_file` with the given
+               parameters
+        Then:
+            - return a tuple of the columns in the CSV file, without the
+              delimiter and quoting
+        """
+        for line, delimiter, quoting, expected in (
+                ('"this","is","a","test"', ",", '"', ("this", "is", "a", "test")),
+                ('"this","is","a","test"', ",", None, ('"this"', '"is"', '"a"', '"test"'))):
+            with self.subTest(line=line, delimiter=delimiter, quoting=quoting):
+                self.assertEqual(
+                    parse_csv_line(
+                        line=line, delimiter=delimiter, quoting=quoting),
+                    expected)
+
+    def test_partition_by(self):
+        """
+        Test that `partition_by` groups the data using the given predicate
+
+        Given:
+          - `part_fn`: a predicate funtion that return boolean True/False
+          - `items`: a sequence of items
+        When:
+          - the partitioning predicate function and the sequence of items are
+            passed to the `partition_by` function
+        Then:
+          - the result is a tuple, with sub-tuples containing the data in the
+            original sequence. Each sub-tuple is a partition, ending as soon as
+            the next value in the sequence, when passed to `part_fn`, returns
+            boolean `True`.
+        """
+        for part_fn, items, expected in (
+                (lambda s: s.startswith("----"),
+                 ("------", "a", "b", "-----", "c", "----", "d", "e", "---",
+                  "f"),
+                 (("------", "a", "b"), ("-----", "c"),
+                  ("----", "d", "e", "---", "f"))),
+                (lambda x: (x % 2) == 0,
+                 (0, 1, 3, 2, 4, 5, 7, 6, 9, 1),
+                 ((0, 1, 3), (2,), (4, 5, 7), (6, 9, 1))),):
+            with self.subTest(items=items):
+                self.assertEqual(partition_by(part_fn, items), expected)
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py
index 7b66688..a88341b 100644
--- a/tests/unit/test_heatmaps.py
+++ b/tests/unit/test_heatmaps.py
@@ -1,46 +1,18 @@
 """Module contains tests for gn3.heatmaps.heatmaps"""
 from unittest import TestCase
+
+from numpy.testing import assert_allclose
+
 from gn3.heatmaps import (
     cluster_traits,
     get_loci_names,
     get_lrs_from_chr,
-    export_trait_data,
     compute_traits_order,
     retrieve_samples_and_values,
     process_traits_data_for_heatmap)
 from tests.unit.sample_test_data import organised_trait_1, organised_trait_2
 
 samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
-trait_data = {
-    "mysqlid": 36688172,
-    "data": {
-        "B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
-        "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
-        "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
-        "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
-        "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
-        "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
-        "BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
-        "BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
-        "BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
-        "BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
-        "BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
-        "BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
-        "BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
-        "BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
-        "BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
-        "BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
-        "BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
-        "BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
-        "BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
-        "BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
-        "BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
-        "BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
-        "BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
-        "BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
-        "C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
-        "C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
-        "DBA/2J": {"sample_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
 
 slinked = (
     (((0, 2, 0.16381088984330505),
@@ -55,63 +27,7 @@ slinked = (
 class TestHeatmap(TestCase):
     """Class for testing heatmap computation functions"""
 
-    def test_export_trait_data_dtype(self):
-        """
-        Test `export_trait_data` with different values for the `dtype` keyword
-        argument
-        """
-        for dtype, expected in [
-                ["val", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["var", (None, None, None, None, None, None)],
-                ["N", (None, None, None, None, None, None)],
-                ["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
-            with self.subTest(dtype=dtype):
-                self.assertEqual(
-                    export_trait_data(trait_data, samplelist, dtype=dtype),
-                    expected)
-
-    def test_export_trait_data_dtype_all_flags(self):
-        """
-        Test `export_trait_data` with different values for the `dtype` keyword
-        argument and the different flags set up
-        """
-        for dtype, vflag, nflag, expected in [
-                ["val", False, False,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["val", False, True,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["val", True, False,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["val", True, True,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["var", False, False, (None, None, None, None, None, None)],
-                ["var", False, True, (None, None, None, None, None, None)],
-                ["var", True, False, (None, None, None, None, None, None)],
-                ["var", True, True, (None, None, None, None, None, None)],
-                ["N", False, False, (None, None, None, None, None, None)],
-                ["N", False, True, (None, None, None, None, None, None)],
-                ["N", True, False, (None, None, None, None, None, None)],
-                ["N", True, True, (None, None, None, None, None, None)],
-                ["all", False, False,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["all", False, True,
-                 (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
-                  8.30401, None, 7.80944, None)],
-                ["all", True, False,
-                 (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
-                  8.30401, None, 7.80944, None)],
-                ["all", True, True,
-                 (7.51879, None, None, 7.77141, None, None, 8.39265, None, None,
-                  8.17443, None, None, 8.30401, None, None, 7.80944, None, None)]
-        ]:
-            with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
-                self.assertEqual(
-                    export_trait_data(
-                        trait_data, samplelist, dtype=dtype, var_exists=vflag,
-                        n_exists=nflag),
-                    expected)
-
-    def test_cluster_traits(self):
+    def test_cluster_traits(self): # pylint: disable=R0201
         """
         Test that the clustering is working as expected.
         """
@@ -126,7 +42,7 @@ class TestHeatmap(TestCase):
             (6.84118, 7.08432, 7.59844, 7.08229, 7.26774, 7.24991),
             (9.45215, 10.6943, 8.64719, 10.1592, 7.75044, 8.78615),
             (7.04737, 6.87185, 7.58586, 6.92456, 6.84243, 7.36913)]
-        self.assertEqual(
+        assert_allclose(
             cluster_traits(traits_data_list),
             ((0.0, 0.20337048635536847, 0.16381088984330505, 1.7388553629398245,
               1.5025235756329178, 0.6952839500255574, 1.271661230252733,