Add methods for working with csv data

gn3/csvcmp.py: New file
(create_dirs_if_not_exists): From a list of dirs, create them if they don't
exist.
(remove_insignificant_edits): Given a dict with a "Modification" key, remove
edits with "delta < ε".
(csv_diff): Generate a csv_diff using the "csvdiff" tool packaged in guix.

tests/unit/test_csvcmp.py: Add some tests for "gn3/csvcmp.py"

2 files changed, 109 insertions, 0 deletions

diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py
new file mode 100644
index 0000000..e033396
--- /dev/null
+++ b/gn3/csvcmp.py
@@ -0,0 +1,68 @@
+import json
+import os
+import uuid
+from gn3.commands import run_cmd
+
+
+def create_dirs_if_not_exists(dirs: list):
+    for dir_ in dirs:
+        if not os.path.exists(dir_):
+            os.makedirs(dir_)
+
+
+def remove_insignificant_edits(diff_data, epsilon=0.001):
+    _mod = []
+    for mod in diff_data.get("Modifications"):
+        original = mod.get("Original").split(",")
+        current = mod.get("Current").split(",")
+        for i, (x, y) in enumerate(zip(original, current)):
+            if all([
+                    x.replace('.', '').isdigit(),
+                    y.replace('.', '').isdigit(),
+                    abs(float(x) - float(y)) < epsilon,
+            ]):
+                current[i] = x
+        if not (__o := ",".join(original)) == (__c := ",".join(current)):
+            _mod.append({
+                "Original": __o,
+                "Current": __c,
+            })
+    diff_data['Modifications'] = _mod
+    return diff_data
+
+
+def csv_diff(base_csv, delta_csv, tmp_dir="/tmp"):
+    base_csv_list = base_csv.strip().split("\n")
+    delta_csv_list = delta_csv.strip().split("\n")
+
+    _header1, _header2 = "", ""
+    for i, line in enumerate(base_csv_list):
+        if line.startswith("Strain Name,Value,SE,Count"):
+            _header1, _header2 = line, delta_csv_list[i]
+            break
+
+    if _header1 != _header2:
+        header = max(_header1, _header2)
+        base_csv = base_csv.replace("Strain Name,Value,SE,Count",
+                                    header, 1)
+        delta_csv = delta_csv.replace("Strain Name,Value,SE,Count",
+                                      header, 1)
+    file_name1 = os.path.join(tmp_dir, str(uuid.uuid4()))
+    file_name2 = os.path.join(tmp_dir, str(uuid.uuid4()))
+    with open(file_name1, "w") as f_:
+        f_.write(base_csv)
+    with open(file_name2, "w") as f_:
+        f_.write(delta_csv)
+
+    # Now we can run the diff!
+    _r = run_cmd(cmd=("csvdiff "
+                      f"'{file_name1}' '{file_name2}' "
+                      "--format json"))
+    if _r.get("code") == 0:
+        _r["output"] = json.loads(_r.get("output"))
+    # Clean Up!
+    if os.path.exists(file_name1):
+        os.remove(file_name1)
+    if os.path.exists(file_name2):
+        os.remove(file_name2)
+    return _r
diff --git a/tests/unit/test_csvcmp.py b/tests/unit/test_csvcmp.py
new file mode 100644
index 0000000..f73865d
--- /dev/null
+++ b/tests/unit/test_csvcmp.py
@@ -0,0 +1,41 @@
+from gn3.csvcmp import csv_diff
+from gn3.csvcmp import remove_insignificant_edits
+
+import pytest
+
+
+@pytest.mark.unit_test
+def test_remove_insignificant_data():
+    diff_data = {
+        'Additions': [],
+        'Deletions': [],
+        'Modifications': [
+            {'Current': '1.000001,3', 'Original': '1,3'},
+            {'Current': '1,3', 'Original': '1.000001,3'},
+            {'Current': '2.000001,3', 'Original': '2,2'},
+            {'Current': '1.01,3', 'Original': '1,2'}
+        ]
+    }
+    expected_json = {
+        'Additions': [],
+        'Deletions': [],
+        'Modifications': [
+            {'Current': '2,3', 'Original': '2,2'},
+            {'Current': '1.01,3', 'Original': '1,2'}
+        ]
+    }
+    assert (remove_insignificant_edits(diff_data) ==
+            expected_json)
+
+
+@pytest.mark.unit_test
+def test_csv_diff():
+    test_results = csv_diff(base_csv="a,b\n1,2\n",
+                            delta_csv="a,b\n1,3")
+    _json = {
+        'Additions': [],
+        'Deletions': [],
+        'Modifications': [{'Current': '1,3', 'Original': '1,2'}]
+    }
+    assert(test_results.get("code") == 0 and
+           test_results.get("output") == _json)