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-rw-r--r--gn3/db/traits.py91
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()))