initial commit for creating dataset

1 files changed, 66 insertions, 0 deletions

diff --git a/gn3/computations/datasets.py b/gn3/computations/datasets.py
new file mode 100644
index 0000000..92a7bdf
--- /dev/null
+++ b/gn3/computations/datasets.py
@@ -0,0 +1,66 @@
+"""module contains the code all related to datasets"""
+from unittest import mock
+
+from typing import Optional
+from typing import List
+
+
+def retrieve_trait_sample_data(dataset_id, dataset_type: str, trait_name: str) -> List:
+    """given the dataset id and trait_name fetch the\
+    sample_name,value from the dataset"""
+
+    # should pass the db as arg all  do a setup
+
+    _func_args = (dataset_id, dataset_type, trait_name)
+    dataset_query = get_query_for_dataset_sample(dataset_type)
+
+    if dataset_query:
+        if dataset_type == "Publish":
+            formatted_query = dataset_query % (trait_name, dataset_id)
+            results = fetch_from_db_sample_data(formatted_query, mock.Mock())
+            return results
+
+        return []
+
+    return []
+
+
+def fetch_from_db_sample_data(formatted_query: str, database_instance) -> List:
+    """this is the function that does the actual fetching of\
+    results from the database"""
+    cursor = database_instance.cursor()
+    cursor.execute(formatted_query)
+    results = cursor.fetchall()
+
+    cursor.close()
+
+    return results
+
+
+def get_query_for_dataset_sample(dataset_type) -> Optional[str]:
+    """this functions contains querys for\
+    getting sample data from the db depending in
+    dataset"""
+    dataset_query = {}
+
+    pheno_query = """
+                SELECT
+                        Strain.Name, PublishData.value, PublishSE.error,NStrain.count, Strain.Name2
+                FROM
+                        (PublishData, Strain, PublishXRef, PublishFreeze)
+                left join PublishSE on
+                        (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
+                left join NStrain on
+                        (NStrain.DataId = PublishData.Id AND
+                        NStrain.StrainId = PublishData.StrainId)
+                WHERE
+                        PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+                        PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
+                        PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id
+                Order BY
+                        Strain.Name
+                """
+
+    dataset_query["Publish"] = pheno_query
+
+    return dataset_query.get(dataset_type)