From 71cc35e5178904b512b9007e33be17a36f6656f2 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 22 Sep 2021 08:36:11 +0300
Subject: Fix typing issues

* Ignore some errors
* Update typing definitions for some portions of code
* Add missing imports
---
 gn3/app.py                    |  2 +-
 gn3/computations/qtlreaper.py |  6 ++++--
 gn3/db/genotypes.py           | 10 ++++++----
 gn3/db/traits.py              |  8 ++++----
 gn3/heatmaps.py               |  8 +++-----
 5 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/gn3/app.py b/gn3/app.py
index 8badb65..5e852e1 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -5,7 +5,7 @@ from typing import Dict
 from typing import Union
 
 from flask import Flask
-from flask_cors import CORS
+from flask_cors import CORS # type: ignore
 
 from gn3.api.gemma import gemma
 from gn3.api.rqtl import rqtl
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 5d17fed..5ddea76 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -4,6 +4,8 @@ computation of QTLs.
 """
 import os
 import subprocess
+from typing import Union
+
 from gn3.random import random_string
 from gn3.settings import TMPDIR, REAPER_COMMAND
 
@@ -70,9 +72,9 @@ def run_reaper(
         output_dir, random_string(10))
     output_list = ["--main_output", output_filename]
     if separate_nperm_output:
-        permu_output_filename = "{}/qtlreaper/permu_output_{}.txt".format(
+        permu_output_filename: Union[None, str] = "{}/qtlreaper/permu_output_{}.txt".format(
             output_dir, random_string(10))
-        output_list = output_list + ["--permu_output", permu_output_filename]
+        output_list = output_list + ["--permu_output", permu_output_filename] # type: ignore[list-item]
     else:
         permu_output_filename = None
 
diff --git a/gn3/db/genotypes.py b/gn3/db/genotypes.py
index 919c539..9ea9f20 100644
--- a/gn3/db/genotypes.py
+++ b/gn3/db/genotypes.py
@@ -2,6 +2,8 @@
 
 import os
 import gzip
+from typing import Union, TextIO
+
 from gn3.settings import GENOTYPE_FILES
 
 def build_genotype_file(
@@ -44,17 +46,17 @@ def __load_genotype_samples_from_geno(genotype_filename: str):
     """
     gzipped_filename = "{}.gz".format(genotype_filename)
     if os.path.isfile(gzipped_filename):
-        genofile = gzip.open(gzipped_filename)
+        genofile: Union[TextIO, gzip.GzipFile] = gzip.open(gzipped_filename)
     else:
         genofile = open(genotype_filename)
 
     for row in genofile:
         line = row.strip()
-        if (not line) or (line.startswith(("#", "@"))):
+        if (not line) or (line.startswith(("#", "@"))): # type: ignore[arg-type]
             continue
         break
 
-    headers = line.split("\t")
+    headers = line.split("\t" ) # type: ignore[arg-type]
     if headers[3] == "Mb":
         return headers[4:]
     return headers[3:]
@@ -107,7 +109,7 @@ def parse_genotype_header(line: str, parlist: tuple = tuple()):
         ("prgy", prgy),
         ("nprgy", len(prgy)))
 
-def parse_genotype_marker(line: str, geno_obj: dict, parlist: list):
+def parse_genotype_marker(line: str, geno_obj: dict, parlist: tuple):
     """
     Parse a data line in a genotype file
 
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 747ed27..4fc47c3 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -63,22 +63,22 @@ def update_sample_data(conn: Any,
     with conn.cursor() as cursor:
         # Update the Strains table
         cursor.execute(STRAIN_ID_SQL, (strain_name, strain_id))
-        updated_strains: int = cursor.rowcount
+        updated_strains = cursor.rowcount
         # Update the PublishData table
         cursor.execute(PUBLISH_DATA_SQL,
                        (None if value == "x" else value,
                         strain_id, publish_data_id))
-        updated_published_data: int = cursor.rowcount
+        updated_published_data = cursor.rowcount
         # Update the PublishSE table
         cursor.execute(PUBLISH_SE_SQL,
                        (None if error == "x" else error,
                         strain_id, publish_data_id))
-        updated_se_data: int = cursor.rowcount
+        updated_se_data = cursor.rowcount
         # Update the NStrain table
         cursor.execute(N_STRAIN_SQL,
                        (None if count == "x" else count,
                         strain_id, publish_data_id))
-        updated_n_strains: int = cursor.rowcount
+        updated_n_strains = cursor.rowcount
     return (updated_strains, updated_published_data,
             updated_se_data, updated_n_strains)
 
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index 9d82fb2..45d0c22 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -7,9 +7,9 @@ from functools import reduce
 from typing import Any, Dict, Sequence
 
 import numpy as np
-import plotly.graph_objects as go
-import plotly.figure_factory as ff
-from plotly.subplots import make_subplots
+import plotly.graph_objects as go # type: ignore
+import plotly.figure_factory as ff # type: ignore
+from plotly.subplots import make_subplots # type: ignore
 
 from gn3.settings import TMPDIR
 from gn3.random import random_string
@@ -171,8 +171,6 @@ def build_heatmap(traits_names, conn: Any):
     clustered = cluster_traits(exported_traits_data_list)
     slinked = slink(clustered)
     traits_order = compute_traits_order(slinked)
-    ordered_traits_names = [
-        traits[idx]["trait_fullname"] for idx in traits_order]
     strains_and_values = retrieve_strains_and_values(
         traits_order, strains, exported_traits_data_list)
     traits_filename = "{}/traits_test_file_{}.txt".format(
-- 
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