Refactor: Move common sample data to separate file

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* Move common sample test data into a separate file where it can be imported
  from, to prevent pylint error R0801 which proved tricky to silence in any
  other way.

4 files changed, 134 insertions, 156 deletions

diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
index d420470..742d106 100644
--- a/tests/unit/computations/test_qtlreaper.py
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -4,6 +4,7 @@ from gn3.computations.qtlreaper import (
     parse_reaper_main_results,
     organise_reaper_main_results,
     parse_reaper_permutation_results)
+from tests.unit.sample_test_data import organised_trait_1
 
 class TestQTLReaper(TestCase):
     """Class for testing qtlreaper interface functions."""
@@ -81,99 +82,54 @@ class TestQTLReaper(TestCase):
         self.assertEqual(
             organise_reaper_main_results([
                 {
-                    "ID": "T1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+                    "ID": "1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
                     "Mb": 3.010, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
+                    "ID": "1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
                     "Mb": 3.492, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
+                    "ID": "1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
                     "Mb": 3.511, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
+                    "ID": "1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
                     "Mb": 3.660, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
+                    "ID": "1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
                     "Mb": 3.777, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
+                    "ID": "1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
                     "Mb": 3.812, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
+                    "ID": "1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
                     "Mb": 4.431, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs51852623", "Chr": 2, "cM": 2.010,
+                    "ID": "1", "Locus": "rs51852623", "Chr": 2, "cM": 2.010,
                     "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140,
+                    "ID": "1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140,
                     "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 },
                 {
-                    "ID": "T1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
+                    "ID": "1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
                     "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 }
             ]),
-            {"T1": {"ID": "T1",
-                    "chromosomes": {
-                        1: {"Chr": 1,
-                            "loci": [
-                                {
-                                    "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                }]},
-                        2: {"Chr": 2,
-                            "loci": [
-                                {
-                                    "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                }]}}}})
+            organised_trait_1)
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index baa2af3..8af8e82 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -170,12 +170,15 @@ class TestTraitsDBFunctions(TestCase):
         db_mock = mock.MagicMock()
 
         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")
+        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")
 
         with db_mock.cursor() as cursor:
             type(cursor).rowcount = 1
diff --git a/tests/unit/sample_test_data.py b/tests/unit/sample_test_data.py
new file mode 100644
index 0000000..407d074
--- /dev/null
+++ b/tests/unit/sample_test_data.py
@@ -0,0 +1,111 @@
+"""
+This module holds a collection of sample data variables, used in more than one
+ test.
+
+This is mostly to avoid the `duplicate-code` pylint error that gets raised if
+the same data is defined in more than one file. It has been found that adding
+the `# pylint: disable=R0801` or `# pylint: disable=duplicate-code` to the top
+of the file seems to not work as expected.
+
+Adding these same declarations to .pylintrc is not an option, since that,
+seemingly, would deactivate the warnings for all code in the project: We do not
+want that.
+"""
+
+organised_trait_1 = {
+    "1": {
+        "ID": "1",
+        "chromosomes": {
+            1: {"Chr": 1,
+                "loci": [
+                    {
+                        "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    }]},
+            2: {"Chr": 2,
+                "loci": [
+                    {
+                        "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    }]}}}}
+
+organised_trait_2 = {
+    "2": {
+        "ID": "2",
+        "chromosomes": {
+            1: {"Chr": 1,
+                "loci": [
+                    {
+                        "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    }]},
+            2: {"Chr": 2,
+                "loci": [
+                    {
+                        "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
+                        "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                    },
+                    {
+                        "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
+                        "LRS": 0.579, "Additive": -0.074, "pValue": 1.000
+                    }]}}}}
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py
index c0a496b..fd91cf9 100644
--- a/tests/unit/test_heatmaps.py
+++ b/tests/unit/test_heatmaps.py
@@ -7,6 +7,7 @@ from gn3.heatmaps import (
     compute_traits_order,
     retrieve_strains_and_values,
     process_traits_data_for_heatmap)
+from tests.unit.sample_test_data import organised_trait_1, organised_trait_2
 
 strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
 trait_data = {
@@ -206,100 +207,7 @@ class TestHeatmap(TestCase):
         """Check for correct processing of data for heatmap generation."""
         self.assertEqual(
             process_traits_data_for_heatmap(
-                {"1": {
-                    "ID": "T1",
-                    "chromosomes": {
-                        1: {"Chr": 1,
-                            "loci": [
-                                {
-                                    "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                }]},
-                        2: {"Chr": 2,
-                            "loci": [
-                                {
-                                    "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                },
-                                {
-                                    "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
-                                    "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                }]}}},
-                 "2": {
-                     "ID": "T1",
-                     "chromosomes": {
-                         1: {"Chr": 1,
-                             "loci": [
-                                 {
-                                     "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 },
-                                 {
-                                     "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 },
-                                 {
-                                     "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 },
-                                 {
-                                     "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 },
-                                 {
-                                     "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 },
-                                 {
-                                     "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 },
-                                 {
-                                     "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 }]},
-                         2: {"Chr": 2,
-                             "loci": [
-                                 {
-                                     "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 },
-                                 {
-                                     "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
-                                     "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
-                                 },
-                                 {
-                                     "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
-                                     "LRS": 0.579, "Additive": -0.074, "pValue": 1.000
-                                 }]}}}},
+                {**organised_trait_1, **organised_trait_2},
                 ["2", "1"],
                 [1, 2]),
             [[[0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],