From 5745c3bdd086f7c499ee63a580df822db5af2826 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 18 May 2021 19:43:50 +0000
Subject: Added unit test for computations/rqtl.py

---
 tests/unit/computations/test_rqtl.py | 41 ++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 tests/unit/computations/test_rqtl.py

(limited to 'tests/unit')

diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py
new file mode 100644
index 0000000..b16f136
--- /dev/null
+++ b/tests/unit/computations/test_rqtl.py
@@ -0,0 +1,41 @@
+"""Test cases for procedures defined in computations.rqtl"""
+import unittest
+
+from unittest import mock
+from gn3.computations.rqtl import generate_rqtl_cmd
+
+class TestRqtl(unittest.TestCase):
+    """Test cases for computations.rqtl module"""
+    @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
+    @mock.patch("gn3.computations.rqtl.get_hash_of_files")
+    def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
+        """Test computing mapping results with R/qtl"""
+        mock_get_hash_files.return_value = "my-hash1"
+        mock_generate_hash_string.return_value = "my-hash2"
+
+        self.assertEqual(
+            generate_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
+                              rqtl_wrapper_kwargs={
+                                  "g": "genofile",
+                                  "p": "phenofile",
+                                  "model": "normal",
+                                  "method": "hk",
+                                  "nperm": 1000,
+                                  "scale": "Mb",
+                                  "control": "rs123456"
+                              },
+                              rqtl_wrapper_bool_kwargs=[
+                                  "addcovar",
+                                  "interval"
+                              ]), {
+                                  "output_file":
+                                  "my-hash1my-hash2my-hash2-output.json",
+                                  "rqtl_cmd": (
+                                      "rqtl-wrapper "
+                                      "--g genofile --p phenofile "
+                                      "--model normal --method hk "
+                                      "--nperm 1000 --scale Mb "
+                                      "--control rs123456 "
+                                      "--addcovar --interval"
+                                  )
+                              })
-- 
cgit v1.2.3


From d66b71a1e149ccddbbcc66e439067250827e0b6f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 18 May 2021 20:06:57 +0000
Subject: Added test for compose_rqtl_cmd in tests/unit/test_commands.py

---
 tests/unit/test_commands.py | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'tests/unit')

diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py
index aafb3a2..a3d0273 100644
--- a/tests/unit/test_commands.py
+++ b/tests/unit/test_commands.py
@@ -6,6 +6,7 @@ from datetime import datetime
 from typing import Callable
 from unittest import mock
 from gn3.commands import compose_gemma_cmd
+from gn3.commands import compose_rqtl_cmd
 from gn3.commands import queue_cmd
 from gn3.commands import run_cmd
 from gn3.exceptions import RedisConnectionError
@@ -53,6 +54,31 @@ class TestCommands(unittest.TestCase):
              "-p /tmp/gf13Ad0tRX/phenofile.txt"
              " -gk"))
 
+    def test_compose_rqtl_cmd(self):
+        """Test that the R/qtl cmd is composed correctly"""
+        self.assertEqual(
+            compose_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
+                             rqtl_wrapper_kwargs={
+                                 "g": "genofile",
+                                 "p": "phenofile",
+                                 "model": "normal",
+                                 "method": "hk",
+                                 "nperm": 1000,
+                                 "scale": "Mb",
+                                 "control": "rs123456"
+                             },
+                             rqtl_wrapper_bool_kwargs=[
+                                 "addcovar",
+                                 "interval"
+                             ]),
+            ("rqtl-wrapper "
+             "--g genofile --p phenofile "
+             "--model normal --method hk "
+             "--nperm 1000 --scale Mb "
+             "--control rs123456 "
+             "--addcovar --interval")
+        )
+
     def test_queue_cmd_exception_raised_when_redis_is_down(self):
         """Test that the correct error is raised when Redis is unavailable"""
         self.assertRaises(RedisConnectionError,
-- 
cgit v1.2.3


From c73c4d4edf88d2af5636962f1e4710be17516ea1 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 17 May 2021 14:34:25 +0300
Subject: tests: test_phenotypes: New test cases for loading phenotypes

---
 tests/unit/db/test_phenotypes.py | 41 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 tests/unit/db/test_phenotypes.py

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
new file mode 100644
index 0000000..8b810fe
--- /dev/null
+++ b/tests/unit/db/test_phenotypes.py
@@ -0,0 +1,41 @@
+"""Tests for db/phenotypes.py"""
+from unittest import TestCase
+from unittest import mock
+
+from gn3.db.phenotypes import Phenotype
+from gn3.db.phenotypes import update_phenotype
+
+
+class TestPhenotypes(TestCase):
+    """Test cases for fetching chromosomes"""
+    def test_update_phenotype_with_no_data(self):
+        """
+        Test that a phenotype is updated correctly if an empty Phenotype dataclass
+        is provided
+        """
+        db_mock = mock.MagicMock()
+        self.assertEqual(update_phenotype(
+            db_mock, data=Phenotype(), where=Phenotype()), None)
+
+    def test_update_phenotype_with_data(self):
+        """
+        Test that a phenotype is updated correctly if some
+        data is provided
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            type(cursor).rowcount = 1
+            self.assertEqual(update_phenotype(
+                db_mock, data=Phenotype(
+                    pre_pub_description="Test Pre Pub",
+                    submitter="Rob",
+                    post_pub_description="Test Post Pub"),
+                where=Phenotype(id_=1)), 1)
+            cursor.execute.assert_called_once_with(
+                "UPDATE Phenotype SET "
+                "Pre_publication_description = "
+                "'Test Pre Pub', "
+                "Post_publication_description = "
+                "'Test Post Pub', Submitter = 'Rob' "
+                "WHERE id = '1'"
+            )
-- 
cgit v1.2.3


From 856d4a72ace3584b731a7c45470e3df2704be02f Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 May 2021 22:12:45 +0300
Subject: db: phenotypes: Update failing tests

---
 tests/unit/db/test_phenotypes.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
index 8b810fe..6b394d7 100644
--- a/tests/unit/db/test_phenotypes.py
+++ b/tests/unit/db/test_phenotypes.py
@@ -3,19 +3,20 @@ from unittest import TestCase
 from unittest import mock
 
 from gn3.db.phenotypes import Phenotype
-from gn3.db.phenotypes import update_phenotype
+from gn3.db.phenotypes import update
 
 
 class TestPhenotypes(TestCase):
     """Test cases for fetching chromosomes"""
     def test_update_phenotype_with_no_data(self):
-        """
-        Test that a phenotype is updated correctly if an empty Phenotype dataclass
+        """Test that a phenotype is updated correctly if an empty Phenotype dataclass
         is provided
+
         """
         db_mock = mock.MagicMock()
-        self.assertEqual(update_phenotype(
-            db_mock, data=Phenotype(), where=Phenotype()), None)
+        self.assertEqual(update(
+            conn=db_mock, table="Phenotype",
+            data=Phenotype(), where=Phenotype()), None)
 
     def test_update_phenotype_with_data(self):
         """
@@ -25,8 +26,9 @@ class TestPhenotypes(TestCase):
         db_mock = mock.MagicMock()
         with db_mock.cursor() as cursor:
             type(cursor).rowcount = 1
-            self.assertEqual(update_phenotype(
-                db_mock, data=Phenotype(
+            self.assertEqual(update(
+                conn=db_mock, table="Phenotype",
+                data=Phenotype(
                     pre_pub_description="Test Pre Pub",
                     submitter="Rob",
                     post_pub_description="Test Post Pub"),
-- 
cgit v1.2.3


From 786d48ede007f0134081495f3f63be3a33b8f71e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 20 May 2021 21:26:34 +0300
Subject: tests: test_phenotype: Add function that tests "fetchone"

---
 tests/unit/db/test_phenotypes.py | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
index 6b394d7..9fed524 100644
--- a/tests/unit/db/test_phenotypes.py
+++ b/tests/unit/db/test_phenotypes.py
@@ -2,6 +2,7 @@
 from unittest import TestCase
 from unittest import mock
 
+from gn3.db.phenotypes import fetchone
 from gn3.db.phenotypes import Phenotype
 from gn3.db.phenotypes import update
 
@@ -41,3 +42,24 @@ class TestPhenotypes(TestCase):
                 "'Test Post Pub', Submitter = 'Rob' "
                 "WHERE id = '1'"
             )
+
+    def test_fetch_phenotype(self):
+        """Test that a single phenotype is fetched properly
+
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            test_data = (
+                35, "Test pre-publication", "Test post-publication",
+                "Original description A", "cm^2", "pre-abbrev",
+                "post-abbrev", "LAB001", "R. W.", "R. W.", "R. W."
+            )
+            cursor.fetchone.return_value = test_data
+            phenotype = fetchone(db_mock,
+                                 "Phenotype",
+                                 where=Phenotype(id_=35))
+            self.assertEqual(phenotype.id_, 35)
+            self.assertEqual(phenotype.pre_pub_description,
+                             "Test pre-publication")
+            cursor.execute.assert_called_once_with(
+                "SELECT * FROM Phenotype WHERE id = '35'")
-- 
cgit v1.2.3


From 93ab68fe650eed0bb53d77225f47f72e527e48c4 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 26 May 2021 12:05:08 +0300
Subject: Move the methods, "update" and "fetch", to gn3.db

---
 gn3/db/__init__.py               | 70 ++++++++++++++++++++++++++++++++++++++++
 gn3/db/phenotypes.py             | 64 ++----------------------------------
 tests/unit/db/test_phenotypes.py |  4 +--
 3 files changed, 74 insertions(+), 64 deletions(-)

(limited to 'tests/unit')

diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
index e69de29..fae4d29 100644
--- a/gn3/db/__init__.py
+++ b/gn3/db/__init__.py
@@ -0,0 +1,70 @@
+# pylint: disable=[R0902, R0903]
+"""Module that exposes common db operations"""
+from typing import Optional, Dict, Any
+from dataclasses import dataclass, asdict, astuple
+from typing_extensions import Protocol
+from MySQLdb import escape_string
+
+from gn3.db.phenotypes import Phenotype
+from gn3.db.phenotypes import PublishXRef
+from gn3.db.phenotypes import Publication
+
+from gn3.db.phenotypes import phenotype_mapping
+from gn3.db.phenotypes import publish_x_ref_mapping
+from gn3.db.phenotypes import publication_mapping
+
+TABLEMAP = {
+    "Phenotype": phenotype_mapping,
+    "PublishXRef": publish_x_ref_mapping,
+    "Publication": publication_mapping,
+}
+
+DATACLASSMAP = {
+    "Phenotype": Phenotype,
+    "PublishXRef": PublishXRef,
+    "Publication": Publication,
+}
+
+
+class Dataclass(Protocol):
+    """Type Definition for a Dataclass"""
+    __dataclass_fields__: Dict
+
+
+def update(conn: Any,
+           table: str,
+           data: Dataclass,
+           where: Dataclass) -> Optional[int]:
+    """Run an UPDATE on a table"""
+    if not any(astuple(data) + astuple(where)):
+        return None
+    sql = f"UPDATE {table} SET "
+    sql += ", ".join(f"{TABLEMAP[table].get(k)} "
+                     f"= '{escape_string(str(v)).decode('utf-8')}'" for
+                     k, v in asdict(data).items()
+                     if v is not None and k in TABLEMAP[table])
+    sql += " WHERE "
+    sql += "AND ".join(f"{TABLEMAP[table].get(k)} = "
+                       f"'{escape_string(str(v)).decode('utf-8')}'" for
+                       k, v in asdict(where).items()
+                       if v is not None and k in TABLEMAP[table])
+    with conn.cursor() as cursor:
+        cursor.execute(sql)
+        return cursor.rowcount
+
+
+def fetchone(conn: Any,
+             table: str,
+             where: Dataclass) -> Optional[Dataclass]:
+    """Run a SELECT on a table. Returns only one result!"""
+    if not any(astuple(where)):
+        return None
+    sql = f"SELECT * FROM {table} "
+    sql += "WHERE "
+    sql += "AND ".join(f"{TABLEMAP[table].get(k)} = "
+                       f"'{escape_string(str(v)).decode('utf-8')}'" for
+                       k, v in asdict(where).items()
+                       if v is not None and k in TABLEMAP[table])
+    with conn.cursor() as cursor:
+        cursor.execute(sql)
+        return DATACLASSMAP[table](*cursor.fetchone())
diff --git a/gn3/db/phenotypes.py b/gn3/db/phenotypes.py
index ee523ad..2b93c85 100644
--- a/gn3/db/phenotypes.py
+++ b/gn3/db/phenotypes.py
@@ -1,17 +1,9 @@
 # pylint: disable=[R0902, R0903]
 """This contains all the necessary functions that access the phenotypes from
 the db"""
-from dataclasses import dataclass, asdict, astuple
+from dataclasses import dataclass
 
-from typing import Any, Dict, Optional
-from MySQLdb import escape_string
-
-from typing_extensions import Protocol
-
-
-class Dataclass(Protocol):
-    """Type Definition for a Dataclass"""
-    __dataclass_fields__: Dict
+from typing import Optional
 
 
 @dataclass(frozen=True)
@@ -107,55 +99,3 @@ publication_mapping = {
     "month": "Month",
     "year": "Year",
 }
-
-
-TABLEMAP = {
-    "Phenotype": phenotype_mapping,
-    "PublishXRef": publish_x_ref_mapping,
-    "Publication": publication_mapping,
-}
-
-DATACLASSMAP = {
-    "Phenotype": Phenotype,
-    "PublishXRef": PublishXRef,
-    "Publication": Publication,
-}
-
-
-def update(conn: Any,
-           table: str,
-           data: Dataclass,
-           where: Dataclass) -> Optional[int]:
-    """Run an UPDATE on a table"""
-    if not any(astuple(data) + astuple(where)):
-        return None
-    sql = f"UPDATE {table} SET "
-    sql += ", ".join(f"{TABLEMAP[table].get(k)} "
-                     f"= '{escape_string(str(v)).decode('utf-8')}'" for
-                     k, v in asdict(data).items()
-                     if v is not None and k in TABLEMAP[table])
-    sql += " WHERE "
-    sql += "AND ".join(f"{TABLEMAP[table].get(k)} = "
-                       f"'{escape_string(str(v)).decode('utf-8')}'" for
-                       k, v in asdict(where).items()
-                       if v is not None and k in TABLEMAP[table])
-    with conn.cursor() as cursor:
-        cursor.execute(sql)
-        return cursor.rowcount
-
-
-def fetchone(conn: Any,
-             table: str,
-             where: Dataclass) -> Optional[Dataclass]:
-    """Run a SELECT on a table. Returns only one result!"""
-    if not any(astuple(where)):
-        return None
-    sql = f"SELECT * FROM {table} "
-    sql += "WHERE "
-    sql += "AND ".join(f"{TABLEMAP[table].get(k)} = "
-                       f"'{escape_string(str(v)).decode('utf-8')}'" for
-                       k, v in asdict(where).items()
-                       if v is not None and k in TABLEMAP[table])
-    with conn.cursor() as cursor:
-        cursor.execute(sql)
-        return DATACLASSMAP[table](*cursor.fetchone())
diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
index 9fed524..505714a 100644
--- a/tests/unit/db/test_phenotypes.py
+++ b/tests/unit/db/test_phenotypes.py
@@ -2,9 +2,9 @@
 from unittest import TestCase
 from unittest import mock
 
-from gn3.db.phenotypes import fetchone
+from gn3.db import fetchone
+from gn3.db import update
 from gn3.db.phenotypes import Phenotype
-from gn3.db.phenotypes import update
 
 
 class TestPhenotypes(TestCase):
-- 
cgit v1.2.3


From 07464f44f48895cc31ba2b088d6125e7777e1073 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sun, 30 May 2021 13:26:15 +0300
Subject: fix index error (#16)

---
 gn3/computations/correlations.py            | 2 +-
 tests/unit/computations/test_correlation.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'tests/unit')

diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index 25dd26d..f0ce502 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -247,7 +247,7 @@ def fetch_lit_correlation_data(
             cursor.execute(query_formatter(query,
                                            *tuple(reversed(query_values))))
             lit_corr_results = cursor.fetchone()
-        lit_results = (gene_id, lit_corr_results[1])\
+        lit_results = (gene_id, lit_corr_results[0])\
             if lit_corr_results else (gene_id, 0)
         return lit_results
     return (gene_id, 0)
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index d264738..5746adf 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -276,7 +276,7 @@ class TestCorrelation(TestCase):
          input trait mouse gene id and mouse gene id
         """
 
-        expected_db_results = [("val", x*0.1)
+        expected_db_results = [[x*0.1]
                                for x in range(1, 4)]
         conn = DataBase(expected_results=expected_db_results)
         expected_results = ("1", 0.1)
-- 
cgit v1.2.3


From ece41f5f971595c5d005c4beaa984c45471a6647 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 2 Jun 2021 07:54:35 +0300
Subject: Get the diff between 2 dicts and return that as a dict

---
 gn3/db/__init__.py               | 16 ++++++++++++++++
 tests/unit/db/test_phenotypes.py |  8 ++++++++
 2 files changed, 24 insertions(+)

(limited to 'tests/unit')

diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
index 1eb7b12..19135fc 100644
--- a/gn3/db/__init__.py
+++ b/gn3/db/__init__.py
@@ -68,3 +68,19 @@ def fetchone(conn: Any,
     with conn.cursor() as cursor:
         cursor.execute(sql)
         return DATACLASSMAP[table](*cursor.fetchone())
+
+
+def diff_from_dict(old: Dict, new: Dict) -> Dict:
+    """Construct a new dict with a specific structure that contains the difference
+between the 2 dicts in the structure:
+
+diff_from_dict({"id": 1, "data": "a"}, {"id": 2, "data": "b"})
+
+Should return:
+
+{"id": {"old": 1, "new": 2}, "data": {"old": "a", "new": "b"}}
+    """
+    dict_ = {}
+    for key, value in old.items():
+        dict_[key] = {"old": old[key], "new": new[key]}
+    return dict_
diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
index 505714a..b53db23 100644
--- a/tests/unit/db/test_phenotypes.py
+++ b/tests/unit/db/test_phenotypes.py
@@ -4,6 +4,7 @@ from unittest import mock
 
 from gn3.db import fetchone
 from gn3.db import update
+from gn3.db import diff_from_dict
 from gn3.db.phenotypes import Phenotype
 
 
@@ -63,3 +64,10 @@ class TestPhenotypes(TestCase):
                              "Test pre-publication")
             cursor.execute.assert_called_once_with(
                 "SELECT * FROM Phenotype WHERE id = '35'")
+
+    def test_diff_from_dict(self):
+        """Test that a correct diff is generated"""
+        self.assertEqual(diff_from_dict({"id": 1, "data": "a"},
+                                        {"id": 2, "data": "b"}),
+                         {"id": {"old": 1, "new": 2},
+                          "data": {"old": "a", "new": "b"}})
-- 
cgit v1.2.3


From a2ef9618dbba2d3f0416cbe8a527ed12070aa67e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 2 Jun 2021 08:22:11 +0300
Subject: unit: test_phenotypes: Test for multiple "WHERE" clauses

---
 tests/unit/db/test_phenotypes.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
index b53db23..fdeca5e 100644
--- a/tests/unit/db/test_phenotypes.py
+++ b/tests/unit/db/test_phenotypes.py
@@ -34,14 +34,14 @@ class TestPhenotypes(TestCase):
                     pre_pub_description="Test Pre Pub",
                     submitter="Rob",
                     post_pub_description="Test Post Pub"),
-                where=Phenotype(id_=1)), 1)
+                where=Phenotype(id_=1, owner="Rob")), 1)
             cursor.execute.assert_called_once_with(
                 "UPDATE Phenotype SET "
                 "Pre_publication_description = "
                 "'Test Pre Pub', "
                 "Post_publication_description = "
                 "'Test Post Pub', Submitter = 'Rob' "
-                "WHERE id = '1'"
+                "WHERE id = '1' AND Owner = 'Rob'"
             )
 
     def test_fetch_phenotype(self):
@@ -58,12 +58,12 @@ class TestPhenotypes(TestCase):
             cursor.fetchone.return_value = test_data
             phenotype = fetchone(db_mock,
                                  "Phenotype",
-                                 where=Phenotype(id_=35))
+                                 where=Phenotype(id_=35, owner="Rob"))
             self.assertEqual(phenotype.id_, 35)
             self.assertEqual(phenotype.pre_pub_description,
                              "Test pre-publication")
             cursor.execute.assert_called_once_with(
-                "SELECT * FROM Phenotype WHERE id = '35'")
+                "SELECT * FROM Phenotype WHERE id = '35' AND Owner = 'Rob'")
 
     def test_diff_from_dict(self):
         """Test that a correct diff is generated"""
-- 
cgit v1.2.3


From c96b29e63577f7189afd02df2ced26b150830341 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 3 Jun 2021 11:08:58 +0300
Subject: Add data structures for the table metadata_audit

---
 gn3/db/__init__.py          |  5 +++++
 gn3/db/metadata_audit.py    | 26 ++++++++++++++++++++++++++
 tests/unit/db/test_audit.py | 28 ++++++++++++++++++++++++++++
 3 files changed, 59 insertions(+)
 create mode 100644 gn3/db/metadata_audit.py
 create mode 100644 tests/unit/db/test_audit.py

(limited to 'tests/unit')

diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
index d89dbf4..175a640 100644
--- a/gn3/db/__init__.py
+++ b/gn3/db/__init__.py
@@ -5,21 +5,26 @@ from dataclasses import dataclass, asdict, astuple
 from typing_extensions import Protocol
 from MySQLdb import escape_string
 
+from gn3.db.metadata_audit import MetadataAudit
 from gn3.db.phenotypes import Phenotype
 from gn3.db.phenotypes import PublishXRef
 from gn3.db.phenotypes import Publication
 
+from gn3.db.metadata_audit import metadata_audit_mapping
 from gn3.db.phenotypes import phenotype_mapping
 from gn3.db.phenotypes import publish_x_ref_mapping
 from gn3.db.phenotypes import publication_mapping
 
+
 TABLEMAP = {
+    "metadata_audit": metadata_audit_mapping,
     "Phenotype": phenotype_mapping,
     "PublishXRef": publish_x_ref_mapping,
     "Publication": publication_mapping,
 }
 
 DATACLASSMAP = {
+    "MetadataAudit": MetadataAudit,
     "Phenotype": Phenotype,
     "PublishXRef": PublishXRef,
     "Publication": Publication,
diff --git a/gn3/db/metadata_audit.py b/gn3/db/metadata_audit.py
new file mode 100644
index 0000000..6e22b32
--- /dev/null
+++ b/gn3/db/metadata_audit.py
@@ -0,0 +1,26 @@
+# pylint: disable=[R0902, R0903]
+"""This contains all the necessary functions that access the metadata_audit
+table from the db
+
+"""
+from dataclasses import dataclass
+from typing import Optional
+
+
+@dataclass(frozen=True)
+class MetadataAudit:
+    """Data Type that represents a Phenotype"""
+    dataset_id: int
+    editor: str
+    json_data: str
+    time_stamp: Optional[str] = None
+
+
+# Mapping from the MetadataAudit dataclass to the actual column names in the
+# database
+metadata_audit_mapping = {
+    "dataset_id": "dataset_id",
+    "editor": "editor",
+    "json_data": "json_data",
+    "time_stamp": "time_stamp",
+}
diff --git a/tests/unit/db/test_audit.py b/tests/unit/db/test_audit.py
new file mode 100644
index 0000000..22787bb
--- /dev/null
+++ b/tests/unit/db/test_audit.py
@@ -0,0 +1,28 @@
+"""Tests for db/phenotypes.py"""
+import json
+from unittest import TestCase
+from unittest import mock
+
+from gn3.db import insert
+from gn3.db.metadata_audit import MetadataAudit
+
+
+class TestMetadatAudit(TestCase):
+    """Test cases for fetching chromosomes"""
+
+    def test_insert_into_metadata_audit(self):
+        """Test that data is inserted correctly in the audit table
+
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            type(cursor).rowcount = 1
+            self.assertEqual(insert(
+                conn=db_mock, table="metadata_audit",
+                data=MetadataAudit(dataset_id=35,
+                                   editor="Bonface",
+                                   json_data=json.dumps({"a": "b"}))), 1)
+            cursor.execute.assert_called_once_with(
+                "INSERT INTO metadata_audit ('dataset_id', "
+                "'editor', 'json_data') "
+                'VALUES (\'35\', \'Bonface\', \'{\\"a\\": \\"b\\"}\')')
-- 
cgit v1.2.3


From de834809dbf5f054a5f75c35dbee653cac8311f3 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 3 Jun 2021 21:11:33 +0300
Subject: tests: test_audit: Update test case to check for prepared statements

---
 tests/unit/db/test_audit.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_audit.py b/tests/unit/db/test_audit.py
index 22787bb..1449281 100644
--- a/tests/unit/db/test_audit.py
+++ b/tests/unit/db/test_audit.py
@@ -23,6 +23,6 @@ class TestMetadatAudit(TestCase):
                                    editor="Bonface",
                                    json_data=json.dumps({"a": "b"}))), 1)
             cursor.execute.assert_called_once_with(
-                "INSERT INTO metadata_audit ('dataset_id', "
-                "'editor', 'json_data') "
-                'VALUES (\'35\', \'Bonface\', \'{\\"a\\": \\"b\\"}\')')
+                "INSERT INTO metadata_audit (dataset_id, "
+                "editor, json_data) VALUES (%s, %s, %s)",
+                (35, 'Bonface', '{"a": "b"}'))
-- 
cgit v1.2.3


From 4c9bbe6d4229b79a1bc62cf2f641fbc4c4f00abc Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 3 Jun 2021 21:38:58 +0300
Subject: Use prepared statements for UPDATE sql function

---
 gn3/db/__init__.py               | 16 +++++++++-------
 tests/unit/db/test_phenotypes.py | 10 ++++------
 2 files changed, 13 insertions(+), 13 deletions(-)

(limited to 'tests/unit')

diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
index 8b6bf73..ce92a7d 100644
--- a/gn3/db/__init__.py
+++ b/gn3/db/__init__.py
@@ -43,18 +43,20 @@ def update(conn: Any,
     """Run an UPDATE on a table"""
     if not (any(astuple(data)) and any(astuple(where))):
         return None
+    data_ = {k: v for k, v in asdict(data).items()
+             if v is not None and k in TABLEMAP[table]}
+    where_ = {k: v for k, v in asdict(where).items()
+              if v is not None and k in TABLEMAP[table]}
     sql = f"UPDATE {table} SET "
     sql += ", ".join(f"{TABLEMAP[table].get(k)} "
-                     f"= '{escape_string(str(v)).decode('utf-8')}'" for
-                     k, v in asdict(data).items()
-                     if v is not None and k in TABLEMAP[table])
+                     "= %s" for k in data_.keys())
     sql += " WHERE "
     sql += " AND ".join(f"{TABLEMAP[table].get(k)} = "
-                        f"'{escape_string(str(v)).decode('utf-8')}'" for
-                        k, v in asdict(where).items()
-                        if v is not None and k in TABLEMAP[table])
+                        "%s" for k in where_.keys())
     with conn.cursor() as cursor:
-        cursor.execute(sql)
+        cursor.execute(sql,
+                       tuple(data_.values()) + tuple(where_.values()))
+        conn.commit()
         return cursor.rowcount
 
 
diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
index fdeca5e..21eb757 100644
--- a/tests/unit/db/test_phenotypes.py
+++ b/tests/unit/db/test_phenotypes.py
@@ -37,12 +37,10 @@ class TestPhenotypes(TestCase):
                 where=Phenotype(id_=1, owner="Rob")), 1)
             cursor.execute.assert_called_once_with(
                 "UPDATE Phenotype SET "
-                "Pre_publication_description = "
-                "'Test Pre Pub', "
-                "Post_publication_description = "
-                "'Test Post Pub', Submitter = 'Rob' "
-                "WHERE id = '1' AND Owner = 'Rob'"
-            )
+                "Pre_publication_description = %s, "
+                "Post_publication_description = %s, "
+                "Submitter = %s WHERE id = %s AND Owner = %s",
+                ('Test Pre Pub', 'Test Post Pub', 'Rob', 1, 'Rob'))
 
     def test_fetch_phenotype(self):
         """Test that a single phenotype is fetched properly
-- 
cgit v1.2.3


From 8210c46fde908b8815ab97f2f91039f87365369b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 3 Jun 2021 21:45:25 +0300
Subject: Use prepared statements for FETCH sql function

---
 gn3/db/__init__.py               | 8 ++++----
 tests/unit/db/test_phenotypes.py | 3 ++-
 2 files changed, 6 insertions(+), 5 deletions(-)

(limited to 'tests/unit')

diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
index d62b575..fea43ec 100644
--- a/gn3/db/__init__.py
+++ b/gn3/db/__init__.py
@@ -66,14 +66,14 @@ def fetchone(conn: Any,
     """Run a SELECT on a table. Returns only one result!"""
     if not any(astuple(where)):
         return None
+    where_ = {k: v for k, v in asdict(where).items()
+              if v is not None and k in TABLEMAP[table]}
     sql = f"SELECT * FROM {table} "
     sql += "WHERE "
     sql += " AND ".join(f"{TABLEMAP[table].get(k)} = "
-                        f"'{escape_string(str(v)).decode('utf-8')}'" for
-                        k, v in asdict(where).items()
-                        if v is not None and k in TABLEMAP[table])
+                        "%s" for k in where_.keys())
     with conn.cursor() as cursor:
-        cursor.execute(sql)
+        cursor.execute(sql, tuple(where_.values()))
         return DATACLASSMAP[table](*cursor.fetchone())
 
 
diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
index 21eb757..824d186 100644
--- a/tests/unit/db/test_phenotypes.py
+++ b/tests/unit/db/test_phenotypes.py
@@ -61,7 +61,8 @@ class TestPhenotypes(TestCase):
             self.assertEqual(phenotype.pre_pub_description,
                              "Test pre-publication")
             cursor.execute.assert_called_once_with(
-                "SELECT * FROM Phenotype WHERE id = '35' AND Owner = 'Rob'")
+                "SELECT * FROM Phenotype WHERE id = %s AND Owner = %s",
+                (35, 'Rob'))
 
     def test_diff_from_dict(self):
         """Test that a correct diff is generated"""
-- 
cgit v1.2.3


From 77e7fb0d6a8090770460cc05e1707056b09e6802 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 7 Jun 2021 10:18:22 +0300
Subject: tests: test_phenotype: Rename to test_db

---
 tests/unit/db/test_db.py         | 73 ++++++++++++++++++++++++++++++++++++++++
 tests/unit/db/test_phenotypes.py | 72 ---------------------------------------
 2 files changed, 73 insertions(+), 72 deletions(-)
 create mode 100644 tests/unit/db/test_db.py
 delete mode 100644 tests/unit/db/test_phenotypes.py

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_db.py b/tests/unit/db/test_db.py
new file mode 100644
index 0000000..a3b1d71
--- /dev/null
+++ b/tests/unit/db/test_db.py
@@ -0,0 +1,73 @@
+"""Tests for db/phenotypes.py"""
+from unittest import TestCase
+from unittest import mock
+
+from gn3.db import fetchone
+from gn3.db import update
+from gn3.db import diff_from_dict
+from gn3.db.phenotypes import Phenotype
+
+
+class TestPhenotypes(TestCase):
+    """Test cases for fetching chromosomes"""
+
+    def test_update_phenotype_with_no_data(self):
+        """Test that a phenotype is updated correctly if an empty Phenotype dataclass
+        is provided
+
+        """
+        db_mock = mock.MagicMock()
+        self.assertEqual(update(
+            conn=db_mock, table="Phenotype",
+            data=Phenotype(), where=Phenotype()), None)
+
+    def test_update_phenotype_with_data(self):
+        """
+        Test that a phenotype is updated correctly if some
+        data is provided
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            type(cursor).rowcount = 1
+            self.assertEqual(update(
+                conn=db_mock, table="Phenotype",
+                data=Phenotype(
+                    pre_pub_description="Test Pre Pub",
+                    submitter="Rob",
+                    post_pub_description="Test Post Pub"),
+                where=Phenotype(id_=1, owner="Rob")), 1)
+            cursor.execute.assert_called_once_with(
+                "UPDATE Phenotype SET "
+                "Pre_publication_description = %s, "
+                "Post_publication_description = %s, "
+                "Submitter = %s WHERE id = %s AND Owner = %s",
+                ('Test Pre Pub', 'Test Post Pub', 'Rob', 1, 'Rob'))
+
+    def test_fetch_phenotype(self):
+        """Test that a single phenotype is fetched properly
+
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            test_data = (
+                35, "Test pre-publication", "Test post-publication",
+                "Original description A", "cm^2", "pre-abbrev",
+                "post-abbrev", "LAB001", "R. W.", "R. W.", "R. W."
+            )
+            cursor.fetchone.return_value = test_data
+            phenotype = fetchone(db_mock,
+                                 "Phenotype",
+                                 where=Phenotype(id_=35, owner="Rob"))
+            self.assertEqual(phenotype.id_, 35)
+            self.assertEqual(phenotype.pre_pub_description,
+                             "Test pre-publication")
+            cursor.execute.assert_called_once_with(
+                "SELECT * FROM Phenotype WHERE id = %s AND Owner = %s",
+                (35, 'Rob'))
+
+    def test_diff_from_dict(self):
+        """Test that a correct diff is generated"""
+        self.assertEqual(diff_from_dict({"id": 1, "data": "a"},
+                                        {"id": 2, "data": "b"}),
+                         {"id": {"old": 1, "new": 2},
+                          "data": {"old": "a", "new": "b"}})
diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py
deleted file mode 100644
index 824d186..0000000
--- a/tests/unit/db/test_phenotypes.py
+++ /dev/null
@@ -1,72 +0,0 @@
-"""Tests for db/phenotypes.py"""
-from unittest import TestCase
-from unittest import mock
-
-from gn3.db import fetchone
-from gn3.db import update
-from gn3.db import diff_from_dict
-from gn3.db.phenotypes import Phenotype
-
-
-class TestPhenotypes(TestCase):
-    """Test cases for fetching chromosomes"""
-    def test_update_phenotype_with_no_data(self):
-        """Test that a phenotype is updated correctly if an empty Phenotype dataclass
-        is provided
-
-        """
-        db_mock = mock.MagicMock()
-        self.assertEqual(update(
-            conn=db_mock, table="Phenotype",
-            data=Phenotype(), where=Phenotype()), None)
-
-    def test_update_phenotype_with_data(self):
-        """
-        Test that a phenotype is updated correctly if some
-        data is provided
-        """
-        db_mock = mock.MagicMock()
-        with db_mock.cursor() as cursor:
-            type(cursor).rowcount = 1
-            self.assertEqual(update(
-                conn=db_mock, table="Phenotype",
-                data=Phenotype(
-                    pre_pub_description="Test Pre Pub",
-                    submitter="Rob",
-                    post_pub_description="Test Post Pub"),
-                where=Phenotype(id_=1, owner="Rob")), 1)
-            cursor.execute.assert_called_once_with(
-                "UPDATE Phenotype SET "
-                "Pre_publication_description = %s, "
-                "Post_publication_description = %s, "
-                "Submitter = %s WHERE id = %s AND Owner = %s",
-                ('Test Pre Pub', 'Test Post Pub', 'Rob', 1, 'Rob'))
-
-    def test_fetch_phenotype(self):
-        """Test that a single phenotype is fetched properly
-
-        """
-        db_mock = mock.MagicMock()
-        with db_mock.cursor() as cursor:
-            test_data = (
-                35, "Test pre-publication", "Test post-publication",
-                "Original description A", "cm^2", "pre-abbrev",
-                "post-abbrev", "LAB001", "R. W.", "R. W.", "R. W."
-            )
-            cursor.fetchone.return_value = test_data
-            phenotype = fetchone(db_mock,
-                                 "Phenotype",
-                                 where=Phenotype(id_=35, owner="Rob"))
-            self.assertEqual(phenotype.id_, 35)
-            self.assertEqual(phenotype.pre_pub_description,
-                             "Test pre-publication")
-            cursor.execute.assert_called_once_with(
-                "SELECT * FROM Phenotype WHERE id = %s AND Owner = %s",
-                (35, 'Rob'))
-
-    def test_diff_from_dict(self):
-        """Test that a correct diff is generated"""
-        self.assertEqual(diff_from_dict({"id": 1, "data": "a"},
-                                        {"id": 2, "data": "b"}),
-                         {"id": {"old": 1, "new": 2},
-                          "data": {"old": "a", "new": "b"}})
-- 
cgit v1.2.3


From 92a6ed26a6990fd37b86efe4caa9f6cd2365f476 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 7 Jun 2021 10:21:33 +0300
Subject: tests: test_db: Rename TestPhenotype

---
 tests/unit/db/test_db.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_db.py b/tests/unit/db/test_db.py
index a3b1d71..2e38d4c 100644
--- a/tests/unit/db/test_db.py
+++ b/tests/unit/db/test_db.py
@@ -8,8 +8,8 @@ from gn3.db import diff_from_dict
 from gn3.db.phenotypes import Phenotype
 
 
-class TestPhenotypes(TestCase):
-    """Test cases for fetching chromosomes"""
+class TestCrudMethods(TestCase):
+    """Test cases for CRUD methods"""
 
     def test_update_phenotype_with_no_data(self):
         """Test that a phenotype is updated correctly if an empty Phenotype dataclass
-- 
cgit v1.2.3


From ea90f7d8276ec9df583b94d7d00c128e63f147ef Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 7 Jun 2021 11:16:45 +0300
Subject: tests: test_db: Add a test-case for fetchall

---
 tests/unit/db/test_db.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_db.py b/tests/unit/db/test_db.py
index 2e38d4c..485678f 100644
--- a/tests/unit/db/test_db.py
+++ b/tests/unit/db/test_db.py
@@ -2,10 +2,12 @@
 from unittest import TestCase
 from unittest import mock
 
+from gn3.db import fetchall
 from gn3.db import fetchone
 from gn3.db import update
 from gn3.db import diff_from_dict
 from gn3.db.phenotypes import Phenotype
+from gn3.db.metadata_audit import MetadataAudit
 
 
 class TestCrudMethods(TestCase):
@@ -65,6 +67,35 @@ class TestCrudMethods(TestCase):
                 "SELECT * FROM Phenotype WHERE id = %s AND Owner = %s",
                 (35, 'Rob'))
 
+    def test_fetchall_metadataaudit(self):
+        """Test that multiple metadata_audit entries are fetched properly
+
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            test_data = (
+                35, "Rob", ('{"pages": '
+                            '{"old": "5099-5109", '
+                            '"new": "5099-5110"}, '
+                            '"month": {"old": "July", '
+                            '"new": "June"}, '
+                            '"year": {"old": "2001", '
+                            '"new": "2002"}}'),
+                "2021-06-04 09:01:05"
+            )
+            cursor.fetchall.return_value = (test_data,)
+            metadata = list(fetchall(db_mock,
+                                     "metadata_audit",
+                                     where=MetadataAudit(dataset_id=35,
+                                                         editor="Rob")))[0]
+            self.assertEqual(metadata.dataset_id, 35)
+            self.assertEqual(metadata.time_stamp,
+                             "2021-06-04 09:01:05")
+            cursor.execute.assert_called_once_with(
+                ("SELECT * FROM metadata_audit WHERE "
+                 "dataset_id = %s AND editor = %s"),
+                (35, 'Rob'))
+
     def test_diff_from_dict(self):
         """Test that a correct diff is generated"""
         self.assertEqual(diff_from_dict({"id": 1, "data": "a"},
-- 
cgit v1.2.3


From bb55cf948974d85fb31d2f424f7ee94f7ab5e3d6 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 7 Jun 2021 19:44:00 +0300
Subject: Rename json_data column to json_diff_data

---
 gn3/db/metadata_audit.py    |  2 +-
 sql/metadata_audit.sql      | 12 ++++++------
 tests/unit/db/test_audit.py |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

(limited to 'tests/unit')

diff --git a/gn3/db/metadata_audit.py b/gn3/db/metadata_audit.py
index 8765738..9c4474d 100644
--- a/gn3/db/metadata_audit.py
+++ b/gn3/db/metadata_audit.py
@@ -23,6 +23,6 @@ metadata_audit_mapping = {
     "id_": "id",
     "dataset_id": "dataset_id",
     "editor": "editor",
-    "json_data": "json_data",
+    "json_data": "json_diff_data",
     "time_stamp": "time_stamp",
 }
diff --git a/sql/metadata_audit.sql b/sql/metadata_audit.sql
index 9771e74..514a2fc 100644
--- a/sql/metadata_audit.sql
+++ b/sql/metadata_audit.sql
@@ -20,10 +20,10 @@
 -- This table stores data on diffs when editing a Published dataset's data
 CREATE TABLE metadata_audit (
     PRIMARY KEY (id),
-    id         INTEGER       AUTO_INCREMENT            NOT NULL,
-    dataset_id INTEGER                                 NOT NULL,
-    editor     VARCHAR(255)                            NOT NULL,
-    json_data  VARCHAR(2048)                           NOT NULL,
-    time_stamp timestamp     DEFAULT CURRENT_TIMESTAMP NOT NULL,
-               CHECK (JSON_VALID(json_data))
+    id              INTEGER       AUTO_INCREMENT            NOT NULL,
+    dataset_id      INTEGER                                 NOT NULL,
+    editor          VARCHAR(255)                            NOT NULL,
+    json_diff_data  VARCHAR(2048)                           NOT NULL,
+    time_stamp      timestamp     DEFAULT CURRENT_TIMESTAMP NOT NULL,
+                    CHECK (JSON_VALID(json_diff_data))
 );
diff --git a/tests/unit/db/test_audit.py b/tests/unit/db/test_audit.py
index 1449281..7480169 100644
--- a/tests/unit/db/test_audit.py
+++ b/tests/unit/db/test_audit.py
@@ -24,5 +24,5 @@ class TestMetadatAudit(TestCase):
                                    json_data=json.dumps({"a": "b"}))), 1)
             cursor.execute.assert_called_once_with(
                 "INSERT INTO metadata_audit (dataset_id, "
-                "editor, json_data) VALUES (%s, %s, %s)",
+                "editor, json_diff_data) VALUES (%s, %s, %s)",
                 (35, 'Bonface', '{"a": "b"}'))
-- 
cgit v1.2.3


From b05c273eae3f19387ab0a6afea4277afd52a9378 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 7 Jun 2021 19:44:31 +0300
Subject: db: test_db: Add extra variable in test data for "id"

---
 tests/unit/db/test_db.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

(limited to 'tests/unit')

diff --git a/tests/unit/db/test_db.py b/tests/unit/db/test_db.py
index 485678f..520e781 100644
--- a/tests/unit/db/test_db.py
+++ b/tests/unit/db/test_db.py
@@ -74,15 +74,14 @@ class TestCrudMethods(TestCase):
         db_mock = mock.MagicMock()
         with db_mock.cursor() as cursor:
             test_data = (
-                35, "Rob", ('{"pages": '
-                            '{"old": "5099-5109", '
-                            '"new": "5099-5110"}, '
-                            '"month": {"old": "July", '
-                            '"new": "June"}, '
-                            '"year": {"old": "2001", '
-                            '"new": "2002"}}'),
-                "2021-06-04 09:01:05"
-            )
+                1, 35, "Rob", ('{"pages": '
+                               '{"old": "5099-5109", '
+                               '"new": "5099-5110"}, '
+                               '"month": {"old": "July", '
+                               '"new": "June"}, '
+                               '"year": {"old": "2001", '
+                               '"new": "2002"}}'),
+                "2021-06-04 09:01:05")
             cursor.fetchall.return_value = (test_data,)
             metadata = list(fetchall(db_mock,
                                      "metadata_audit",
-- 
cgit v1.2.3


From 12089cb2eae2201d3b348d21dd0e93a61e16e7c7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 21:27:38 +0000
Subject: Change test_compose_rqtl_command in test_commands.py to have
 different arguments to hopefully avoid github's pylint 'duplicate code'
 complaint

Changed some parameters in test_compose_rqtl_cmd to avoid pylint complaining about duplicate code
---
 tests/unit/test_commands.py | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

(limited to 'tests/unit')

diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py
index a3d0273..aaefb23 100644
--- a/tests/unit/test_commands.py
+++ b/tests/unit/test_commands.py
@@ -59,24 +59,23 @@ class TestCommands(unittest.TestCase):
         self.assertEqual(
             compose_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
                              rqtl_wrapper_kwargs={
-                                 "g": "genofile",
-                                 "p": "phenofile",
-                                 "model": "normal",
-                                 "method": "hk",
-                                 "nperm": 1000,
+                                 "g": "the_genofile",
+                                 "p": "the_phenofile",
+                                 "model": "np",
+                                 "method": "ehk",
+                                 "nperm": 2000,
                                  "scale": "Mb",
-                                 "control": "rs123456"
+                                 "control": "rs234567"
                              },
                              rqtl_wrapper_bool_kwargs=[
-                                 "addcovar",
-                                 "interval"
+                                 "addcovar"
                              ]),
             ("rqtl-wrapper "
-             "--g genofile --p phenofile "
-             "--model normal --method hk "
-             "--nperm 1000 --scale Mb "
-             "--control rs123456 "
-             "--addcovar --interval")
+             "--g the_genofile --p the_phenofile "
+             "--model np --method ehk "
+             "--nperm 2000 --scale Mb "
+             "--control rs234567 "
+             "--addcovar")
         )
 
     def test_queue_cmd_exception_raised_when_redis_is_down(self):
-- 
cgit v1.2.3


From efe73f2f142bd2a12b89ad638c9387cf9c6ded18 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 22:01:21 +0000
Subject: Fixed test_compose_rqtl_command test; forgot to include Rscript in
 the command

---
 tests/unit/test_commands.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'tests/unit')

diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py
index aaefb23..f36ba55 100644
--- a/tests/unit/test_commands.py
+++ b/tests/unit/test_commands.py
@@ -70,7 +70,7 @@ class TestCommands(unittest.TestCase):
                              rqtl_wrapper_bool_kwargs=[
                                  "addcovar"
                              ]),
-            ("rqtl-wrapper "
+            ("Rscript rqtl-wrapper "
              "--g the_genofile --p the_phenofile "
              "--model np --method ehk "
              "--nperm 2000 --scale Mb "
-- 
cgit v1.2.3


From d8c4b1a0188574cdd70638a99e2984b54bec6033 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 22:16:26 +0000
Subject: Fixed test_rqtl.py to include Rscript in the command

---
 tests/unit/computations/test_rqtl.py | 82 ++++++++++++++++++------------------
 1 file changed, 41 insertions(+), 41 deletions(-)

(limited to 'tests/unit')

diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py
index b16f136..3bf8f81 100644
--- a/tests/unit/computations/test_rqtl.py
+++ b/tests/unit/computations/test_rqtl.py
@@ -1,41 +1,41 @@
-"""Test cases for procedures defined in computations.rqtl"""
-import unittest
-
-from unittest import mock
-from gn3.computations.rqtl import generate_rqtl_cmd
-
-class TestRqtl(unittest.TestCase):
-    """Test cases for computations.rqtl module"""
-    @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
-    @mock.patch("gn3.computations.rqtl.get_hash_of_files")
-    def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
-        """Test computing mapping results with R/qtl"""
-        mock_get_hash_files.return_value = "my-hash1"
-        mock_generate_hash_string.return_value = "my-hash2"
-
-        self.assertEqual(
-            generate_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
-                              rqtl_wrapper_kwargs={
-                                  "g": "genofile",
-                                  "p": "phenofile",
-                                  "model": "normal",
-                                  "method": "hk",
-                                  "nperm": 1000,
-                                  "scale": "Mb",
-                                  "control": "rs123456"
-                              },
-                              rqtl_wrapper_bool_kwargs=[
-                                  "addcovar",
-                                  "interval"
-                              ]), {
-                                  "output_file":
-                                  "my-hash1my-hash2my-hash2-output.json",
-                                  "rqtl_cmd": (
-                                      "rqtl-wrapper "
-                                      "--g genofile --p phenofile "
-                                      "--model normal --method hk "
-                                      "--nperm 1000 --scale Mb "
-                                      "--control rs123456 "
-                                      "--addcovar --interval"
-                                  )
-                              })
+"""Test cases for procedures defined in computations.rqtl"""
+import unittest
+
+from unittest import mock
+from gn3.computations.rqtl import generate_rqtl_cmd
+
+class TestRqtl(unittest.TestCase):
+    """Test cases for computations.rqtl module"""
+    @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
+    @mock.patch("gn3.computations.rqtl.get_hash_of_files")
+    def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
+        """Test computing mapping results with R/qtl"""
+        mock_get_hash_files.return_value = "my-hash1"
+        mock_generate_hash_string.return_value = "my-hash2"
+
+        self.assertEqual(
+            generate_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
+                              rqtl_wrapper_kwargs={
+                                  "g": "genofile",
+                                  "p": "phenofile",
+                                  "model": "normal",
+                                  "method": "hk",
+                                  "nperm": 1000,
+                                  "scale": "Mb",
+                                  "control": "rs123456"
+                              },
+                              rqtl_wrapper_bool_kwargs=[
+                                  "addcovar",
+                                  "interval"
+                              ]), {
+                                  "output_file":
+                                  "my-hash1my-hash2my-hash2-output.json",
+                                  "rqtl_cmd": (
+                                      "Rscript rqtl-wrapper "
+                                      "--g genofile --p phenofile "
+                                      "--model normal --method hk "
+                                      "--nperm 1000 --scale Mb "
+                                      "--control rs123456 "
+                                      "--addcovar --interval"
+                                  )
+                              })
-- 
cgit v1.2.3


From 9dca7551ff6c1fa8c3b26ded2c1b63cfab001eca Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 22:21:46 +0000
Subject: Fixed file type from json to csv for test_generate_rqtl_command

---
 tests/unit/computations/test_rqtl.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'tests/unit')

diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py
index 3bf8f81..09790b7 100644
--- a/tests/unit/computations/test_rqtl.py
+++ b/tests/unit/computations/test_rqtl.py
@@ -29,7 +29,7 @@ class TestRqtl(unittest.TestCase):
                                   "interval"
                               ]), {
                                   "output_file":
-                                  "my-hash1my-hash2my-hash2-output.json",
+                                  "my-hash1my-hash2my-hash2-output.csv",
                                   "rqtl_cmd": (
                                       "Rscript rqtl-wrapper "
                                       "--g genofile --p phenofile "
-- 
cgit v1.2.3


From f7becfa11ca857104ecc1b668b4bd3d0a721083c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 22:28:37 +0000
Subject: Fixed another error where test_generate_rqtl_command didn't include
 the filename argument (not sure why running unit tests locally doesn't detect
 this)

---
 tests/unit/computations/test_rqtl.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'tests/unit')

diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py
index 09790b7..955d0ab 100644
--- a/tests/unit/computations/test_rqtl.py
+++ b/tests/unit/computations/test_rqtl.py
@@ -36,6 +36,7 @@ class TestRqtl(unittest.TestCase):
                                       "--model normal --method hk "
                                       "--nperm 1000 --scale Mb "
                                       "--control rs123456 "
+                                      "--filename my-hash1my-hash2my-hash2-output.csv "
                                       "--addcovar --interval"
                                   )
                               })
-- 
cgit v1.2.3