Fix a myriad of linting errors

* Fix linting errors like:

  - Unused variables
  - Undeclared variable errors (mostly caused by typos, and wrong names)
  - Missing documentation strings for functions

  etc.

1 files changed, 12 insertions, 12 deletions

diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
index 5c3e7b8..a1daa3c 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -398,8 +398,8 @@ def fetch_sample_ids(
         "AND Species.name=%(species_name)s")
     with conn.cursor() as cursor:
         cursor.execute(
-            query, samples_names=tuple(samples),
-            species_name=species)
+            query, samples_names=tuple(sample_names),
+            species_name=species_name)
         return cursor.fetchall()
 
 def build_query_sgo_lit_corr(
@@ -419,7 +419,7 @@ def build_query_sgo_lit_corr(
          f" FROM ({db_type}, {db_type}XRef, {db_type}Freeze) " +
          f"LEFT JOIN {temp_table} ON {temp_table}.GeneId2=ProbeSet.GeneId " +
          " ".join(joins) +
-         f" WHERE ProbeSet.GeneId IS NOT NULL " +
+         " WHERE ProbeSet.GeneId IS NOT NULL " +
          f"AND {temp_table}.value IS NOT NULL " +
          f"AND {db_type}XRef.{db_type}FreezeId = {db_type}Freeze.Id " +
          f"AND {db_type}Freeze.Name = %(db_name)s " +
@@ -443,7 +443,7 @@ def build_query_tissue_corr(db_type, temp_table, sample_id_columns, joins):
          f" FROM ({db_type}, {db_type}XRef, {db_type}Freeze) " +
          f"LEFT JOIN {temp_table} ON {temp_table}.Symbol=ProbeSet.Symbol " +
          " ".join(joins) +
-         f" WHERE ProbeSet.Symbol IS NOT NULL " +
+         " WHERE ProbeSet.Symbol IS NOT NULL " +
          f"AND {temp_table}.Correlation IS NOT NULL " +
          f"AND {db_type}XRef.{db_type}FreezeId = {db_type}Freeze.Id " +
          f"AND {db_type}Freeze.Name = %(db_name)s " +
@@ -451,17 +451,17 @@ def build_query_tissue_corr(db_type, temp_table, sample_id_columns, joins):
          f"ORDER BY {db_type}.Id"),
         3)
 
-def fetch_all_database_data(
-        conn: Any, species: str, gene_id: int, gene_symbol: str,
+def fetch_all_database_data(# pylint: disable=[R0913, R0914]
+        conn: Any, species: str, gene_id: int, trait_symbol: str,
         samples: Tuple[str, ...], db_type: str, db_name: str, method: str,
-        returnNumber: int, tissueProbeSetFreezeId: int) -> Tuple[Any, Any]:
+        return_number: int, probeset_freeze_id: int) -> Tuple[Any, Any]:
     """
     This is a migration of the
     `web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function in
     GeneNetwork1.
     """
     def __build_query__(sample_ids, temp_table):
-        sample_id_columns = ", ".join(f"T{smpl}.value" for smpl in samples_ids)
+        sample_id_columns = ", ".join(f"T{smpl}.value" for smpl in sample_ids)
         if db_type == "Publish":
             joins = tuple(
                 ("LEFT JOIN PublishData AS T{item} "
@@ -484,12 +484,12 @@ def fetch_all_database_data(
                 for item in sample_ids)
             if method.lower() == "sgo literature correlation":
                 return build_query_sgo_lit_corr(
-                    sample_ids, temp_table, sample_id_columns)
+                    sample_ids, temp_table, sample_id_columns, joins)
             if method.lower() in (
                     "tissue correlation, pearson's r",
                     "tissue correlation, spearman's rho"):
                 return build_query_tissue_corr(
-                    sample_ids, temp_table, sample_id_columns)
+                    sample_ids, temp_table, sample_id_columns, joins)
         joins = tuple(
             (f"LEFT JOIN {db_type}Data AS T{item} "
              f"ON T{item}.Id = {db_type}XRef.DataId "
@@ -513,7 +513,7 @@ def fetch_all_database_data(
             cursor.execute(
                 query, db_name=db_name,
                 **{f"T{item}_sample_id": item for item in sample_ids})
-            return cursor.fetchall()
+            return (cursor.fetchall(), data_start_pos)
 
     sample_ids = tuple(
         # look into graduating this to an argument and removing the `samples`
@@ -543,4 +543,4 @@ def fetch_all_database_data(
         with conn.cursor() as cursor:
             cursor.execute(f"DROP TEMPORARY TABLE {temp_table}")
 
-    return trait_database, data_start_pos
+    return (tuple(item[0] for item in trait_database), trait_database[0][1])