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-rw-r--r--gn3/computations/correlations.py3
-rw-r--r--gn3/computations/correlations2.py37
-rw-r--r--gn3/computations/slink.py97
-rw-r--r--gn3/db/traits.py159
-rw-r--r--tests/unit/computations/test_correlation.py32
-rw-r--r--tests/unit/computations/test_slink.py401
-rw-r--r--tests/unit/db/test_traits.py126
7 files changed, 624 insertions, 231 deletions
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index bc738a7..56f483c 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -1,4 +1,5 @@
"""module contains code for correlations"""
+import math
import multiprocessing
from typing import List
@@ -90,7 +91,7 @@ def compute_sample_r_correlation(trait_name, corr_method, trait_vals,
target_values=sanitized_target_vals,
corr_method=corr_method)
- if corr_coefficient is not None:
+ if corr_coefficient is not None and not math.isnan(corr_coefficient):
return (trait_name, corr_coefficient, p_value, num_overlap)
return None
diff --git a/gn3/computations/correlations2.py b/gn3/computations/correlations2.py
index 6c456db..93db3fa 100644
--- a/gn3/computations/correlations2.py
+++ b/gn3/computations/correlations2.py
@@ -1,15 +1,25 @@
+"""
+DESCRIPTION:
+ TODO: Add a description for the module
+
+FUNCTIONS:
+compute_correlation:
+ TODO: Describe what the function does..."""
+
from math import sqrt
from functools import reduce
## From GN1: mostly for clustering and heatmap generation
-def items_with_values(dbdata, userdata):
+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"""
+ 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,
@@ -17,19 +27,24 @@ This should probably be renamed to something sensible"""
[[], []])
def compute_correlation(dbdata, userdata):
- x, y = items_with_values(dbdata, userdata)
- if len(x) < 6:
- return (0.0, len(x))
- meanx = sum(x)/len(x)
- meany = sum(y)/len(y)
+ """Compute some form of correlation.
+
+ 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, y), [0.0, 0.0, 0.0])
+ 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))
- except ZeroDivisionError as zde:
- return(0, len(x))
+ return ((xyd/(sqrt(sxd)*sqrt(syd))), len(x_items))
+ except ZeroDivisionError:
+ return(0, len(x_items))
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py
index 8d51f29..23d3d88 100644
--- a/gn3/computations/slink.py
+++ b/gn3/computations/slink.py
@@ -7,13 +7,18 @@ slink:
TODO: Describe what the function does...
"""
import logging
-from functools import partial
+from typing import List, Tuple, Union, Sequence
+
+NumType = Union[int, float]
+SeqOfNums = Sequence[NumType]
class LengthError(BaseException):
- pass
+ """Raised whenever child lists/tuples are not the same length as the parent
+ list of tuple."""
class MirrorError(BaseException):
- pass
+ """Raised if the distance from child A to child B is not the same as the
+ distance from child B to child A."""
def __is_list_or_tuple(item):
return type(item) in [list, tuple]
@@ -50,19 +55,20 @@ def __raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists):
def __raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists):
"""Check that the distance from A to B, is the same as the distance from B to A.
If the two distances are different, throw an exception."""
- for i in range(len(lists)):
- for j in range(len(lists)):
- if lists[i][j] != lists[j][i]:
- raise MirrorError(
- ("Distance from one child({}) to the other ({}) "
- "should be the same in both directions.").format(
- lists[i][j], lists[j][i]))
+ inner_coords = range(len(lists))
+ coords = ((i, j) for i in inner_coords for j in inner_coords)
+ def __is_same_reversed(coord):
+ return lists[coord[0]][coord[1]] == lists[coord[1]][coord[0]]
+ if not all(map(__is_same_reversed, coords)):
+ raise MirrorError((
+ "Distance from one child to the other should be the same in both "
+ "directions."))
def __raise_valueerror_on_negative_distances(lists):
"""Check that distances between 'somethings' are all positive, otherwise,
raise an exception."""
def zero_or_positive(val):
- return val >= 0;
+ return val >= 0
# flatten lists
flattened = __flatten_list_of_lists(lists)
if not all(map(zero_or_positive, flattened)):
@@ -71,12 +77,16 @@ raise an exception."""
def __flatten_list_of_lists(parent):
return [item for child in parent for item in child]
-def nearest(lists, i, j):
+# i and j are Union[SeqOfNums, NumType], but that leads to errors where the
+# values of i or j are indexed, since the NumType type is not indexable.
+# I don't know how to type this so that it does not fail on running `mypy .`
+def nearest(lists: Sequence[SeqOfNums], i, j) -> NumType:
"""
Computes shortest distance between member(s) in `i` and member(s) in `j`.
Description:
- This is 'copied' over from genenetwork1, from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64.
+ This is 'copied' over from genenetwork1, from
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64.
This description should be updated to better describe what 'member' means in
the context where the function is used.
@@ -108,19 +118,25 @@ def nearest(lists, i, j):
__raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists)
__raise_valueerror_on_negative_distances(lists)
#### END: Guard Functions ####
- if type(i) == int and type(j) == int: # From member i to member j
+ if isinstance(i, int) and isinstance(j, int): # From member i to member j
return lists[i][j]
- elif type(i) == int and __is_list_or_tuple(j):
+
+ if isinstance(i, int) and __is_list_or_tuple(j):
return min(map(lambda j_new: nearest(lists, i, j_new), j[:-1]))
- elif type(j) == int and __is_list_or_tuple(i):
+ if isinstance(j, int) and __is_list_or_tuple(i):
return min(map(lambda i_new: nearest(lists, i_new, j), i[:-1]))
- elif __is_list_or_tuple(i) and __is_list_or_tuple(j):
+
+ if __is_list_or_tuple(i) and __is_list_or_tuple(j):
coordinate_pairs = __flatten_list_of_lists(
[[(itemi, itemj) for itemj in j[:-1]] for itemi in i[:-1]])
return min(map(lambda x: nearest(lists, x[0], x[1]), coordinate_pairs))
- else:
- raise ValueError("member values (i or j) should be lists/tuples of integers or integers")
+ raise ValueError("member values (i or j) should be lists/tuples of integers or integers")
+
+# `lists` here could be Sequence[SeqOfNums], but that leads to errors I do not
+# understand down the line
+# Might have to re-implement the function especially since the errors are thrown
+# where `listindexcopy` is involved
def slink(lists):
"""
DESCRIPTION:
@@ -144,36 +160,39 @@ def slink(lists):
"""
try:
size = len(lists)
- listindex = range(size)
listindexcopy = list(range(size))
- listscopy = [[item for item in child] for child in lists]
- initSize = size
+ listscopy = [child[:] for child in lists]
+ init_size = size
candidate = []
- while initSize >2:
+ while init_size > 2:
mindist = 1e10
- for i in range(initSize):
- for j in range(i+1,initSize):
+ for i in range(init_size):
+ for j in range(i+1, init_size):
if listscopy[i][j] < mindist:
- mindist = listscopy[i][j]
- candidate=[[i,j]]
+ mindist = listscopy[i][j]
+ candidate = [[i, j]]
elif listscopy[i][j] == mindist:
- mindist = listscopy[i][j]
- candidate.append([i,j])
+ mindist = listscopy[i][j]
+ candidate.append([i, j])
else:
pass
- newmem = (listindexcopy[candidate[0][0]],listindexcopy[candidate[0][1]],mindist)
+ newmem = (
+ listindexcopy[candidate[0][0]], listindexcopy[candidate[0][1]],
+ mindist)
listindexcopy.pop(candidate[0][1])
listindexcopy[candidate[0][0]] = newmem
- initSize -= 1
- for i in range(initSize):
- for j in range(i+1,initSize):
- listscopy[i][j] = nearest(lists,listindexcopy[i],listindexcopy[j])
+ init_size -= 1
+ for i in range(init_size):
+ for j in range(i+1, init_size):
+ listscopy[i][j] = nearest(
+ lists, listindexcopy[i], listindexcopy[j])
listscopy[j][i] = listscopy[i][j]
- listindexcopy.append(nearest(lists,listindexcopy[0],listindexcopy[1]))
+ listindexcopy.append(
+ nearest(lists, listindexcopy[0], listindexcopy[1]))
return listindexcopy
- except Exception as e:
- # TODO: Look into making the logging log output to the system's
- # configured logger(s)
- logging.warning("Exception: {}, {}".format(type(e), e))
+ except (LengthError, MirrorError, TypeError, IndexError) as exc:
+ # Look into making the logging log output to the system's
+ # configured logger(s)
+ logging.warning("Exception: %s, %s", type(exc), exc)
return []
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index a77e6a1..ae1939a 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,5 +1,5 @@
"""This class contains functions relating to trait data manipulation"""
-from typing import Any, Union
+from typing import Any, Dict, Union
def get_trait_csv_sample_data(conn: Any,
@@ -75,3 +75,160 @@ def update_sample_data(conn: Any,
updated_n_strains: int = cursor.rowcount
return (updated_strains, updated_published_data,
updated_se_data, updated_n_strains)
+
+
+def retrieve_trait_dataset_name(
+ trait_type: str, threshold: int, name: str, connection: Any):
+ """
+ Retrieve the name of a trait given the trait's name
+
+ This is extracted from the `webqtlDataset.retrieveName` function as is
+ implemented at
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169
+ """
+ columns = "Id, Name, FullName, ShortName{}".format(
+ ", DataScale" if trait_type == "ProbeSet" else "")
+ query = (
+ "SELECT {columns} "
+ "FROM {trait_type}Freeze "
+ "WHERE "
+ "public > %(threshold)s "
+ "AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)").format(
+ columns=columns, trait_type=trait_type)
+ with connection.cursor() as cursor:
+ cursor.execute(query, {"threshold": threshold, "name": name})
+ return cursor.fetchone()
+
+PUBLISH_TRAIT_INFO_QUERY = (
+ "SELECT "
+ "PublishXRef.Id, Publication.PubMed_ID, "
+ "Phenotype.Pre_publication_description, "
+ "Phenotype.Post_publication_description, "
+ "Phenotype.Original_description, "
+ "Phenotype.Pre_publication_abbreviation, "
+ "Phenotype.Post_publication_abbreviation, "
+ "Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, "
+ "Phenotype.Authorized_Users, CAST(Publication.Authors AS BINARY), "
+ "Publication.Title, Publication.Abstract, Publication.Journal, "
+ "Publication.Volume, Publication.Pages, Publication.Month, "
+ "Publication.Year, PublishXRef.Sequence, Phenotype.Units, "
+ "PublishXRef.comments "
+ "FROM "
+ "PublishXRef, Publication, Phenotype, PublishFreeze "
+ "WHERE "
+ "PublishXRef.Id = %(trait_name)s AND "
+ "Phenotype.Id = PublishXRef.PhenotypeId AND "
+ "Publication.Id = PublishXRef.PublicationId AND "
+ "PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND "
+ "PublishFreeze.Id =%(trait_dataset_id)s")
+
+
+def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+ """Retrieve trait information for type `Publish` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L399-L421"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ PUBLISH_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_id"]
+ })
+ return cursor.fetchone()
+
+PROBESET_TRAIT_INFO_QUERY = (
+ "SELECT "
+ "ProbeSet.name, ProbeSet.symbol, ProbeSet.description, "
+ "ProbeSet.probe_target_description, ProbeSet.chr, ProbeSet.mb, "
+ "ProbeSet.alias, ProbeSet.geneid, ProbeSet.genbankid, ProbeSet.unigeneid, "
+ "ProbeSet.omim, ProbeSet.refseq_transcriptid, ProbeSet.blatseq, "
+ "ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, "
+ "ProbeSet.strand_probe, ProbeSet.strand_gene, "
+ "ProbeSet.probe_set_target_region, ProbeSet.proteinid, "
+ "ProbeSet.probe_set_specificity, ProbeSet.probe_set_blat_score, "
+ "ProbeSet.probe_set_blat_mb_start, ProbeSet.probe_set_blat_mb_end, "
+ "ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, "
+ "ProbeSet.flag "
+ "FROM "
+ "ProbeSet, ProbeSetFreeze, ProbeSetXRef "
+ "WHERE "
+ "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND "
+ "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND "
+ "ProbeSetFreeze.Name = %(trait_dataset_name)s AND "
+ "ProbeSet.Name = %(trait_name)s")
+
+def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+ """Retrieve trait information for type `ProbeSet` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L424-L435"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ PROBESET_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_name"]
+ })
+ return cursor.fetchone()
+
+GENO_TRAIT_INFO_QUERY = (
+ "SELECT "
+ "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence "
+ "FROM "
+ "Geno, GenoFreeze, GenoXRef "
+ "WHERE "
+ "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND "
+ "GenoFreeze.Name = %(trait_dataset_name)s AND Geno.Name = %(trait_name)s")
+
+def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+ """Retrieve trait information for type `Geno` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ GENO_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name", "trait_dataset_name"]
+ })
+ return cursor.fetchone()
+
+TEMP_TRAIT_INFO_QUERY = (
+ "SELECT name, description FROM Temp "
+ "WHERE Name = %(trait_name)s")
+
+def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any):
+ """Retrieve trait information for type `Temp` traits.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ TEMP_TRAIT_INFO_QUERY,
+ {
+ k:v for k, v in trait_data_source.items()
+ if k in ["trait_name"]
+ })
+ return cursor.fetchone()
+
+def retrieve_trait_info(
+ trait_type: str, trait_name: str, trait_dataset_id: int,
+ trait_dataset_name: str, conn: Any):
+ """Retrieves the trait information.
+
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456
+
+ This function, or the dependent functions, might be incomplete as they are
+ currently."""
+ trait_info_function_table = {
+ "Publish": retrieve_publish_trait_info,
+ "ProbeSet": retrieve_probeset_trait_info,
+ "Geno": retrieve_geno_trait_info,
+ "Temp": retrieve_temp_trait_info
+ }
+ return trait_info_function_table[trait_type](
+ {
+ "trait_name": trait_name,
+ "trait_dataset_id": trait_dataset_id,
+ "trait_dataset_name":trait_dataset_name
+ },
+ conn)
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 6153c8a..9450094 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -467,26 +467,28 @@ class TestCorrelation(TestCase):
self.assertEqual(results, [expected_results])
def test_compute_correlation(self):
- for dbdata,userdata,expected in [
- [[None,None,None,None,None,None,None,None,None,None],
- [None,None,None,None,None,None,None,None,None,None],
+ """Test that the new correlation function works the same as the original
+ from genenetwork1."""
+ for dbdata, userdata, expected in [
+ [[None, None, None, None, None, None, None, None, None, None],
+ [None, None, None, None, None, None, None, None, None, None],
(0.0, 0)],
- [[None,None,None,None,None,None,None,None,None,0],
- [None,None,None,None,None,None,None,None,None,None],
+ [[None, None, None, None, None, None, None, None, None, 0],
+ [None, None, None, None, None, None, None, None, None, None],
(0.0, 0)],
- [[None,None,None,None,None,None,None,None,None,0],
- [None,None,None,None,None,None,None,None,None,0],
+ [[None, None, None, None, None, None, None, None, None, 0],
+ [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, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
(0, 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],
+ [[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)],
- [[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],
+ [[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)],
- [[0,1,2,3,4,5,6,7,8,9],
- [None,None,None,None,2,None,None,3,None,None],
+ [[0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
+ [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)
+ self.assertEqual(compute_correlation(dbdata, userdata), expected)
diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py
index 5627767..995393b 100644
--- a/tests/unit/computations/test_slink.py
+++ b/tests/unit/computations/test_slink.py
@@ -1,5 +1,4 @@
"""Module contains tests for slink"""
-import unittest
from unittest import TestCase
from gn3.computations.slink import slink
@@ -11,210 +10,302 @@ class TestSlink(TestCase):
"""Class for testing slink functions"""
def test_nearest_expects_list_of_lists(self):
+ """Test that function only accepts a list of lists."""
# This might be better handled with type-hints and mypy
for item in [9, "some string", 5.432,
- [1,2,3], ["test", 7.4]]:
+ [1, 2, 3], ["test", 7.4]]:
with self.subTest(item=item):
with self.assertRaises(ValueError, msg="Expected list or tuple"):
nearest(item, 1, 1)
def test_nearest_does_not_allow_empty_lists(self):
+ """Test that function does not accept an empty list, or any of the child
+ lists to be empty."""
for lst in [[],
- [[],[]],
- [[],[],[]],
- [[0, 1, 2],[],[1, 2, 0]]]:
+ [[], []],
+ [[], [], []],
+ [[0, 1, 2], [], [1, 2, 0]]]:
with self.subTest(lst=lst):
with self.assertRaises(ValueError):
nearest(lst, 1, 1)
- def test_nearest_expects_exception_if_all_child_lists_are_not_of_equal_length_to_length_of_parent_list(self):
- for lst in [[[0,1]],
- [[0,1,2],[3,4,5]],
- [[0,1,2,3],[4,5,6],[7,8,9,0]],
- [[0,1,2,3,4],[5,6,7,8,9],[1,2,3,4,5],[2,3],[3,4,5,6,7]]]:
+ def test_nearest_expects_children_are_same_length_as_parent(self):
+ """Test that children lists are same length as parent list."""
+ for lst in [[[0, 1]],
+ [[0, 1, 2], [3, 4, 5]],
+ [[0, 1, 2, 3], [4, 5, 6], [7, 8, 9, 0]],
+ [[0, 1, 2, 3, 4], [5, 6, 7, 8, 9], [1, 2, 3, 4, 5], [2, 3],
+ [3, 4, 5, 6, 7]]]:
with self.subTest(lst=lst):
with self.assertRaises(LengthError):
nearest(lst, 1, 1)
- def test_nearest_expects_exception_if_distance_of_child_from_itself_is_not_zero(self):
+ def test_nearest_expects_member_is_zero_distance_from_itself(self):
+ """Test that distance of a member from itself is zero"""
for lst in [[[1]],
- [[1,2],[3,4]],
- [1,0,0],[0,0,5],[0,3,4],
- [0,0,0,0],[0,0,3,3],[0,1,2,3],[0,3,2,0]]:
+ [[1, 2], [3, 4]],
+ [1, 0, 0], [0, 0, 5], [0, 3, 4],
+ [0, 0, 0, 0], [0, 0, 3, 3], [0, 1, 2, 3], [0, 3, 2, 0]]:
with self.subTest(lst=lst):
with self.assertRaises(ValueError):
nearest(lst, 1, 1)
- def test_nearest_expects_exception_if_distance_from_child_a_to_child_b_is_not_distance_from_child_b_to_child_a(self):
- for lst in [[[0,1],[2,0]],
- [[0,1,2],[1,0,3],[9,7,0]],
- [[0,1,2,3],[7,0,2,3],[2,3,0,1],[8,9,5,0]]]:
+ def test_nearest_expects_distance_atob_is_equal_to_distance_btoa(self):
+ """Test that the distance from member A to member B is the same as that
+ from member B to member A."""
+ for lst in [[[0, 1], [2, 0]],
+ [[0, 1, 2], [1, 0, 3], [9, 7, 0]],
+ [[0, 1, 2, 3], [7, 0, 2, 3], [2, 3, 0, 1], [8, 9, 5, 0]]]:
with self.subTest(lst=lst):
with self.assertRaises(MirrorError):
nearest(lst, 1, 1)
def test_nearest_expects_zero_or_positive_distances(self):
+ """Test that all distances are either zero, or greater than zero."""
# Based on:
# https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L87-L89
- for lst in [[[0,-1,2,3],[-1,0,3,4],[2,3,0,5],[3,4,5,0]],
- [[0,1,-2,3],[1,0,3,4],[-2,3,0,5],[3,4,5,0]],
- [[0,1,2,3],[1,0,-3,4],[2,-3,0,5],[3,4,5,0]],
- [[0,1,2,-3],[1,0,3,4],[2,3,0,5],[-3,4,5,0]],
- [[0,1,2,3],[1,0,3,-4],[2,3,0,5],[3,-4,5,0]],
- [[0,1,2,3],[1,0,3,4],[2,3,0,-5],[3,4,-5,0]]]:
+ for lst in [[[0, -1, 2, 3], [-1, 0, 3, 4], [2, 3, 0, 5], [3, 4, 5, 0]],
+ [[0, 1, -2, 3], [1, 0, 3, 4], [-2, 3, 0, 5], [3, 4, 5, 0]],
+ [[0, 1, 2, 3], [1, 0, -3, 4], [2, -3, 0, 5], [3, 4, 5, 0]],
+ [[0, 1, 2, -3], [1, 0, 3, 4], [2, 3, 0, 5], [-3, 4, 5, 0]],
+ [[0, 1, 2, 3], [1, 0, 3, -4], [2, 3, 0, 5], [3, -4, 5, 0]],
+ [[0, 1, 2, 3], [1, 0, 3, 4], [2, 3, 0, -5], [3, 4, -5, 0]]]:
with self.subTest(lst=lst):
with self.assertRaises(ValueError, msg="Distances should be positive."):
nearest(lst, 1, 1)
def test_nearest_returns_shortest_distance_given_coordinates_to_both_group_members(self):
+ """Test that the shortest distance is returned."""
# This test is named wrong - at least I think it is, from the expected results
# This tests distance when both `i`, and `j` are integers
# We still need to add tests for when (either one/both) (is/are) not (an) integer(s)
# https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L39-L40
- for lst, i, j, expected in [[[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 0,0,0],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 0,1,9],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 0,2,3],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 0,3,6],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 0,4,11],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 1,0,9],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 1,1,0],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 1,2,7],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 1,3,5],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 1,4,10],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 2,0,3],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 2,1,7],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 2,2,0],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 2,3,9],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 2,4,2],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 3,0,6],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 3,1,5],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 3,2,9],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 3,3,0],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 3,4,8],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 4,0,11],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 4,1,10],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 4,2,2],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 4,3,8],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- 4,4,0],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 0,0,0],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 0,1,9],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 0,2,5.5],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 0,3,6],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 0,4,11],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 1,0,9],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 1,1,0],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 1,2,7],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 1,3,5],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 1,4,10],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 2,0,5.5],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 2,1,7],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 2,2,0],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 2,3,9],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 2,4,2],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 3,0,6],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 3,1,5],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 3,2,9],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 3,3,0],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 3,4,3],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 4,0,11],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 4,1,10],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 4,2,2],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 4,3,3],
- [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]],
- 4,4,0]]:
+ for lst, i, j, expected in [
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 0, 0, 0],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 0, 1, 9],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 0, 2, 3],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 0, 3, 6],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 0, 4, 11],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 1, 0, 9],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 1, 1, 0],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 1, 2, 7],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 1, 3, 5],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 1, 4, 10],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 2, 0, 3],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 2, 1, 7],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 2, 2, 0],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 2, 3, 9],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 2, 4, 2],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 3, 0, 6],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 3, 1, 5],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 3, 2, 9],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 3, 3, 0],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 3, 4, 8],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 4, 0, 11],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 4, 1, 10],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 4, 2, 2],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 4, 3, 8],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ 4, 4, 0],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 0, 0, 0],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 0, 1, 9],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 0, 2, 5.5],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 0, 3, 6],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 0, 4, 11],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 1, 0, 9],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 1, 1, 0],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 1, 2, 7],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 1, 3, 5],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 1, 4, 10],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 2, 0, 5.5],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 2, 1, 7],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 2, 2, 0],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 2, 3, 9],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 2, 4, 2],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 3, 0, 6],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 3, 1, 5],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 3, 2, 9],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 3, 3, 0],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 3, 4, 3],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 4, 0, 11],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 4, 1, 10],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 4, 2, 2],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 4, 3, 3],
+ [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2],
+ [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]],
+ 4, 4, 0]]:
with self.subTest(lst=lst):
self.assertEqual(nearest(lst, i, j), expected)
- def test_given_a_list_or_tuple_of_members_distances_and_a_coordinate_find_closest_member_to_member_at_coordinate(self):
- for md, ml, mc, ed in [
- [[[0,9,3],[9,0,7],[3,7,0]],(0,2,3),1,7],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,1,2,3,4],3,0],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,1,2,4],3,5],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,2,4],3,6],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[2,4],3,9]]:
+ def test_nearest_gives_shortest_distance_between_list_of_members_and_member(self):
+ """Test that the shortest distance is returned."""
+ for members_distances, members_list, member_coordinate, expected_distance in [
+ [[[0, 9, 3], [9, 0, 7], [3, 7, 0]], (0, 2, 3), 1, 7],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], [0, 1, 2, 3, 4], 3, 0],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], [0, 1, 2, 4], 3, 5],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], [0, 2, 4], 3, 6],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], [2, 4], 3, 9]]:
with self.subTest(
- members_distances=md, members_list=ml, member_coordinate=mc,
- expected_distance=ed):
- self.assertEqual(nearest(md, ml, mc), ed)
- self.assertEqual(nearest(md, mc, ml), ed)
+ members_distances=members_distances,
+ members_list=members_list,
+ member_coordinate=member_coordinate,
+ expected_distance=expected_distance):
+ self.assertEqual(
+ nearest(
+ members_distances, members_list, member_coordinate),
+ expected_distance)
+ self.assertEqual(
+ nearest(
+ members_distances, member_coordinate, members_list),
+ expected_distance)
- def test_given_2_lists_or_tuples_of_members_distances_nearest_returns_shortest_distance(self):
- for md, ml, mc, ed in [
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- [0,1,2,3,4],[0,1,2,3,4],0],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- [0,1],[3,4],6],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- [0,1],[2,3,4],3],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],
- [0,2],[3,4],6]]:
+ def test_nearest_returns_shortest_distance_given_two_lists_of_members(self):
+ """Test that the shortest distance is returned."""
+ for members_distances, members_list, member_list2, expected_distance in [
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ [0, 1, 2, 3, 4], [0, 1, 2, 3, 4], 0],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ [0, 1], [3, 4], 6],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ [0, 1], [2, 3, 4], 3],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]],
+ [0, 2], [3, 4], 6]]:
with self.subTest(
- members_distances=md, members_list=ml, member_coordinate=mc,
- expected_distance=ed):
- self.assertEqual(nearest(md, ml, mc), ed)
- self.assertEqual(nearest(md, mc, ml), ed)
+ members_distances=members_distances,
+ members_list=members_list,
+ member_list2=member_list2,
+ expected_distance=expected_distance):
+ self.assertEqual(
+ nearest(
+ members_distances, members_list, member_list2),
+ expected_distance)
+ self.assertEqual(
+ nearest(
+ members_distances, member_list2, members_list),
+ expected_distance)
def test_slink_wrong_data_returns_empty_list(self):
+ """Test that empty list is returned for wrong data."""
for data in [1, "test", [], 2.945, nearest, [0]]:
with self.subTest(data=data):
self.assertEqual(slink(data), [])
def test_slink_with_data(self):
+ """Test slink with example data, and expected results for each data
+ sample."""
for data, expected in [
- [[[0,9],[9,0]],[0,1,9]],
- [[[0,9,3],[9,0,7],[3,7,0]],[(0,2,3),1,7]],
- [[[0,9,3,6],[9,0,7,5],[3,7,0,9],[6,5,9,0]],[(0,2,3),(1,3,5),6]],
- [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],
- [11,10,2,8,0]],
- [(0,(2,4,2),3),(1,3,5),6]]]:
+ [[[0, 9], [9, 0]], [0, 1, 9]],
+ [[[0, 9, 3], [9, 0, 7], [3, 7, 0]], [(0, 2, 3), 1, 7]],
+ [[[0, 9, 3, 6], [9, 0, 7, 5], [3, 7, 0, 9], [6, 5, 9, 0]],
+ [(0, 2, 3), (1, 3, 5), 6]],
+ [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2],
+ [6, 5, 9, 0, 8],
+ [11, 10, 2, 8, 0]],
+ [(0, (2, 4, 2), 3), (1, 3, 5), 6]]]:
with self.subTest(data=data):
self.assertEqual(slink(data), expected)
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 0e69bbe..c8f28b5 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -1,12 +1,120 @@
-"""Tests for db/traits.py"""
-from unittest import TestCase
-from unittest import mock
+"""Tests for gn3/db/traits.py"""
+from unittest import mock, TestCase
+from gn3.db.traits import (
+ GENO_TRAIT_INFO_QUERY,
+ TEMP_TRAIT_INFO_QUERY,
+ PUBLISH_TRAIT_INFO_QUERY,
+ PROBESET_TRAIT_INFO_QUERY)
+from gn3.db.traits import (
+ retrieve_trait_info,
+ retrieve_geno_trait_info,
+ retrieve_temp_trait_info,
+ retrieve_trait_dataset_name,
+ retrieve_publish_trait_info,
+ retrieve_probeset_trait_info,
+ update_sample_data)
-from gn3.db.traits import update_sample_data
+class TestTraitsDBFunctions(TestCase):
+ "Test cases for traits functions"
+
+ def test_retrieve_trait_dataset_name(self):
+ """Test that the function is called correctly."""
+ for trait_type, thresh, trait_dataset_name, columns in [
+ ["ProbeSet", 9, "testName",
+ "Id, Name, FullName, ShortName, DataScale"],
+ ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName"],
+ ["Publish", 6, "publishTraitName",
+ "Id, Name, FullName, ShortName"],
+ ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName"]]:
+ db_mock = mock.MagicMock()
+ with self.subTest(trait_type=trait_type):
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = (
+ "testName", "testNameFull", "testNameShort",
+ "dataScale")
+ self.assertEqual(
+ retrieve_trait_dataset_name(
+ trait_type, thresh, trait_dataset_name, db_mock),
+ ("testName", "testNameFull", "testNameShort",
+ "dataScale"))
+ cursor.execute.assert_called_once_with(
+ "SELECT {cols} "
+ "FROM {ttype}Freeze "
+ "WHERE public > %(threshold)s AND "
+ "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format(
+ cols=columns, ttype=trait_type),
+ {"threshold": thresh, "name": trait_dataset_name})
+
+ def test_retrieve_publish_trait_info(self):
+ """Test retrieval of type `Publish` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "PublishTraitName", "trait_dataset_id": 1}
+ self.assertEqual(
+ retrieve_publish_trait_info(
+ trait_source,
+ db_mock),
+ tuple())
+ cursor.execute.assert_called_once_with(
+ PUBLISH_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_probeset_trait_info(self):
+ """Test retrieval of type `Probeset` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "ProbeSetTraitName",
+ "trait_dataset_name": "ProbeSetDatasetTraitName"}
+ self.assertEqual(
+ retrieve_probeset_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ PROBESET_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_geno_trait_info(self):
+ """Test retrieval of type `Geno` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {
+ "trait_name": "GenoTraitName",
+ "trait_dataset_name": "GenoDatasetTraitName"}
+ self.assertEqual(
+ retrieve_geno_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ GENO_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_temp_trait_info(self):
+ """Test retrieval of type `Temp` traits."""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ trait_source = {"trait_name": "TempTraitName"}
+ self.assertEqual(
+ retrieve_temp_trait_info(trait_source, db_mock), tuple())
+ cursor.execute.assert_called_once_with(
+ TEMP_TRAIT_INFO_QUERY, trait_source)
+
+ def test_retrieve_trait_info(self):
+ """Test that information on traits is retrieved as appropriate."""
+ for trait_type, trait_name, trait_dataset_id, trait_dataset_name, in [
+ ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName"],
+ ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName"],
+ ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName"],
+ ["Temp", "TempTraitName", 4, "TempDatasetTraitName"]]:
+ db_mock = mock.MagicMock()
+ with self.subTest(trait_type=trait_type):
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = tuple()
+ self.assertEqual(
+ retrieve_trait_info(
+ trait_type, trait_name, trait_dataset_id,
+ trait_dataset_name, db_mock),
+ tuple())
-class TestTraitsSqlMethods(TestCase):
- """Test cases for sql operations that affect traits"""
def test_update_sample_data(self):
"""Test that the SQL queries when calling update_sample_data are called with
the right calls.
@@ -14,12 +122,12 @@ class TestTraitsSqlMethods(TestCase):
"""
db_mock = mock.MagicMock()
- STRAIN_ID_SQL: str = "UPDATE Strain SET Name = '%s' WHERE Id = %s"
+ 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 DataId = %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' "
+ N_STRAIN_SQL: str = ("UPDATE NStrain SET count = %s "
"WHERE StrainId = %s AND DataId = %s")
with db_mock.cursor() as cursor:
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 17:09:27 +0000