1 files changed, 0 insertions, 91 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 4860a07..a773fb2 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,92 +1 @@
-"""This contains all the necessary functions that are required to add traits
-to the published database"""
-from dataclasses import dataclass
-from typing import Any, Dict, Optional
-
-
-@dataclass(frozen=True)
-class Riset:
-    """Class for keeping track of riset. A riset is a group e.g. rat HSNIH-Palmer,
-BXD
-
-    """
-    name: Optional[str]
-    r_id: Optional[int]
-
-
-@dataclass(frozen=True)
-class WebqtlCaseData:
-    """Class for keeping track of one case data in one trait"""
-    value: Optional[float] = None
-    variance: Optional[float] = None
-    count: Optional[int] = None  # Number of Individuals
-
-    def __str__(self):
-        _str = ""
-        if self.value:
-            _str += f"value={self.value:.3f}"
-        if self.variance:
-            _str += f" variance={self.variance:.3f}"
-        if self.count:
-            _str += " n_data={self.count}"
-        return _str
-
-
-def lookup_webqtldataset_name(riset_name: str, conn: Any):
-    """Given a group name(riset), return it's name e.g. BXDPublish,
-HLCPublish."""
     with conn.cursor() as cursor:
-        cursor.execute(
-            "SELECT PublishFreeze.Name FROM "
-            "PublishFreeze, InbredSet WHERE "
-            "PublishFreeze.InbredSetId = InbredSet.Id "
-            "AND InbredSet.Name = '%s'" % riset_name)
-        _result, *_ = cursor.fetchone()
-        return _result
-
-
-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, "
-                 "PublishFreeze WHERE PublishFreeze.InbredSetId = "
-                 "InbredSet.Id AND PublishFreeze.Name = '%s'" % name)
-    elif data_type == "Geno":
-        query = ("SELECT InbredSet.Name, InbredSet.Id FROM InbredSet, "
-                 "GenoFreeze WHERE GenoFreeze.InbredSetId = "
-                 "InbredSet.Id AND GenoFreeze.Name = '%s'" % name)
-    elif data_type == "ProbeSet":
-        query = ("SELECT InbredSet.Name, InbredSet.Id FROM "
-                 "InbredSet, ProbeSetFreeze, ProbeFreeze WHERE "
-                 "ProbeFreeze.InbredSetId = InbredSet.Id AND "
-                 "ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND "
-                 "ProbeSetFreeze.Name = '%s'" % name)
-    if query:
-        with conn.cursor() as cursor:
-            _name, _id = cursor.fetchone()
-            if _name == "BXD300":
-                _name = "BXD"
-    return Riset(_name, _id)
-
-
-def insert_publication(pubmed_id: int, publication: Optional[Dict],
-                       conn: Any):
-    """Creates a new publication record if it's not available"""
-    sql = ("SELECT Id FROM Publication where "
-           "PubMed_ID = %d" % pubmed_id)
-    _id = None
-    with conn.cursor() as cursor:
-        cursor.execute(sql)
-        _id = cursor.fetchone()
-    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)" %
-                        (", ".join(publication.keys()),
-                         ", ".join(['%s'] * len(publication))))
-        with conn.cursor() as cursor:
-            cursor.execute(insert_query, tuple(publication.values()))