From 83dfbe112f32511b4f656de7f387470cff0680ed Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 5 May 2021 14:37:35 +0300
Subject: Fix pep-8 errors

---
 gn3/api/data_entry.py |  2 ++
 gn3/db/traits.py      | 67 +++++++++------------------------------------------
 gn3/db_utils.py       |  3 +--
 3 files changed, 14 insertions(+), 58 deletions(-)

(limited to 'gn3')

diff --git a/gn3/api/data_entry.py b/gn3/api/data_entry.py
index e69a6cb..0a093d1 100644
--- a/gn3/api/data_entry.py
+++ b/gn3/api/data_entry.py
@@ -9,10 +9,12 @@ data_entry = Blueprint("data_entry", __name__)
 @data_entry.route("/phenotype", methods=["POST"],
                   strict_slashes=False)
 def load_phenotype():
+    """Load the phenotype"""
     return jsonify("Pass")
 
 
 @data_entry.route("/genotype", methods=["POST"],
                   strict_slashes=False)
 def load_genotype():
+    """Load the genotype"""
     return jsonify("Pass")
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 0cebe2c..4860a07 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,23 +1,21 @@
 """This contains all the necessary functions that are required to add traits
 to the published database"""
 from dataclasses import dataclass
-from itertools import chain
-from typing import Optional
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, Optional
 
 
 @dataclass(frozen=True)
-class riset:
+class Riset:
     """Class for keeping track of riset. A riset is a group e.g. rat HSNIH-Palmer,
 BXD
 
     """
-    name: str
-    r_id: int
+    name: Optional[str]
+    r_id: Optional[int]
 
 
 @dataclass(frozen=True)
-class webqtlCaseData:
+class WebqtlCaseData:
     """Class for keeping track of one case data in one trait"""
     value: Optional[float] = None
     variance: Optional[float] = None
@@ -48,6 +46,10 @@ HLCPublish."""
 
 
 def get_riset(data_type: str, name: str, conn: Any):
+    """Get the groups given the data type and it's PublishFreeze or GenoFreeze
+name
+
+    """
     query, _name, _id = None, None, None
     if data_type == "Publish":
         query = ("SELECT InbredSet.Name, InbredSet.Id FROM InbredSet, "
@@ -68,7 +70,7 @@ def get_riset(data_type: str, name: str, conn: Any):
             _name, _id = cursor.fetchone()
             if _name == "BXD300":
                 _name = "BXD"
-    return riset(_name, _id)
+    return Riset(_name, _id)
 
 
 def insert_publication(pubmed_id: int, publication: Optional[Dict],
@@ -80,7 +82,7 @@ def insert_publication(pubmed_id: int, publication: Optional[Dict],
     with conn.cursor() as cursor:
         cursor.execute(sql)
         _id = cursor.fetchone()
-    if not _id:
+    if not _id and publication:
         # The Publication contains the fields: 'authors', 'title', 'abstract',
         # 'journal','volume','pages','month','year'
         insert_query = ("INSERT into Publication (%s) Values (%s)" %
@@ -88,50 +90,3 @@ def insert_publication(pubmed_id: int, publication: Optional[Dict],
                          ", ".join(['%s'] * len(publication))))
         with conn.cursor() as cursor:
             cursor.execute(insert_query, tuple(publication.values()))
-
-
-def insert_publication_data(riset_id: int, strains: List, conn: Any):
-    species_id = None
-    with conn.cursor() as cursor:
-        cursor.execute("SELECT SpeciesId from InbredSet where "
-                       "Id=%s" % riset_id)
-        species_id, *_ = cursor.fetchone()
-        cursor.execute(
-            "SELECT Id FROM Strain WHERE SpeciesId="
-            "%s AND Name in (%s)"
-            % (riset_id, ", ".join(f"'{strain}'" for strain in strains)))
-        strain_ids = cursor.fetchall()
-        data_id, *_ = cursor.execute("SELECT max(Id) "
-                                     "from PublishData").fetchone()
-
-        if strain_ids:
-            strain_ids = list(chain(*strain_ids))
-        for strain, strain_id in zip(strains, strain_ids):
-            # TODO: Fetch this values correctly using sql
-            value, variance, trait_np = 1, 1, 1
-            if value:
-                cursor.execute(
-                    "INSERT INTO PublishData values (%d, %d, %s)" %
-                    (data_id, strain_id, value))
-            if variance:
-                cursor.execute(
-                    "INSERT INTO PublishSE values (%d, %d, %s)" %
-                    (data_id, strain_id, variance))
-            if trait_np:
-                cursor.execute(
-                    "INSERT INTO NStrain values (%d, %d, %s)" %
-                    (data_id, strain_id, trait_np))
-        inbred_set_id = lookup_webqtldataset_name(riset_name="",
-                                                  conn=conn)
-        cursor.execute(
-            "SELECT max(Sequence) FROM PublishXRef where "
-            "InbredSetId = %d and PhenotypeId = %d and PublicationId = %d" %
-            (inbred_set_id, phenotype_id, publication_id))
-
-
-def insert_phenotype(phenotype: Optional[Dict], conn: Any):
-    insert_query = ("INSERT into Phenotype (%s) Values (%s)" %
-                    (", ".join(phenotype.keys()),
-                     ", ".join(['%s'] * len(phenotype))))
-    with conn.cursor() as cursor:
-        cursor.execute(insert_query, tuple(phenotype.values()))
diff --git a/gn3/db_utils.py b/gn3/db_utils.py
index 34c5bf0..9dd3215 100644
--- a/gn3/db_utils.py
+++ b/gn3/db_utils.py
@@ -14,11 +14,10 @@ def parse_db_url() -> Tuple:
             parsed_db.password, parsed_db.path[1:])
 
 
-def database_connector()->Tuple:
+def database_connector() -> Tuple:
     """function to create db connector"""
     host, user, passwd, db_name = parse_db_url()
     conn = mdb.connect(host, user, passwd, db_name)
     cursor = conn.cursor()
 
     return (conn, cursor)
-    
\ No newline at end of file
-- 
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