add mysqlclient in guix

add env variable for GN2_URL

3 files changed, 24 insertions, 1 deletions

diff --git a/gn3/computations/datasets.py b/gn3/computations/datasets.py
index 8e9d743..28d40a1 100644
--- a/gn3/computations/datasets.py
+++ b/gn3/computations/datasets.py
@@ -204,3 +204,23 @@ def create_dataset(dataset_type=None, dataset_name: str = None):
     results = dataset_creator(
         dataset_name=dataset_name, dataset_type=dataset_type)
     return results
+
+
+def fetch_dataset_sample_id(samplelist: List, database, species: str) -> dict:
+    """fetch the strain ids from the db only if\
+    it is in the samplelist"""
+    # xtodo create an in clause for samplelist
+
+    strain_query = """
+        SELECT Strain.Name, Strain.Id FROM Strain, Species
+        WHERE Strain.Name IN {}
+        and Strain.SpeciesId=Species.Id
+        and Species.name = '{}'
+        """
+
+    database_cursor = database.cursor()
+    database_cursor.execute(strain_query.format(samplelist, species))
+
+    results = database_cursor.fetchall()
+
+    return dict(results)
diff --git a/gn3/settings.py b/gn3/settings.py
index 2836581..d9d4f90 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -15,3 +15,6 @@ TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir())
 SQLALCHEMY_DATABASE_URI = "mysql://kabui:1234@localhost/test"
 SECRET_KEY = "password"
 SQLALCHEMY_TRACK_MODIFICATIONS = False
+# gn2 results only used in fetching dataset info
+
+GN2_BASE_URL = "http://www.genenetwork.org/"
diff --git a/guix.scm b/guix.scm
index 4f4e3b2..a810a12 100644
--- a/guix.scm
+++ b/guix.scm
@@ -78,7 +78,7 @@
                        ("python-pylint" python-pylint)
                        ("python-redis" ,python-redis)
                        ("python-scipy" ,python-scipy)
-                       ("python-scipy" ,python-scipy)
+                       ("python-mysqlclient" ,python-mysqlclient)
                        ("python-sqlalchemy-stubs" ,python-sqlalchemy-stubs)))
   (build-system python-build-system)
   (home-page "https://github.com/genenetwork/genenetwork3")