removing conditional db connections

Author: antgonza

qiita_db/analysis.py

@@ -663,8 +663,7 @@ def build_files(self, rarefaction_depth=None):
 
     def _get_samples(self, conn_handler=None):
         """Retrieves dict of samples to proc_data_id for the analysis"""
-        conn_handler = conn_handler if conn_handler is not None \
-            else SQLConnectionHandler()
+        conn_handler = SQLConnectionHandler()
         sql = ("SELECT processed_data_id, array_agg(sample_id ORDER BY "
                "sample_id) FROM qiita.analysis_sample WHERE analysis_id = %s "
                "GROUP BY processed_data_id")
@@ -701,8 +700,7 @@ def _build_biom_tables(self, samples, rarefaction_depth,
                 new_tables[data_type] = new_tables[data_type].merge(table)
 
         # add the new tables to the analysis
-        conn_handler = conn_handler if conn_handler is not None \
-            else SQLConnectionHandler()
+        conn_handler = SQLConnectionHandler()
         _, base_fp = get_mountpoint(self._table)[0]
         for dt, biom_table in viewitems(new_tables):
             # rarefy, if specified
@@ -719,9 +717,7 @@ def _build_biom_tables(self, samples, rarefaction_depth,
     def _build_mapping_file(self, samples, conn_handler=None):
         """Builds the combined mapping file for all samples
            Code modified slightly from qiime.util.MetadataMap.__add__"""
-        conn_handler = conn_handler if conn_handler is not None \
-            else SQLConnectionHandler()
-
+        conn_handler = SQLConnectionHandler()
         all_sample_ids = set()
         sql = """SELECT filepath_id, filepath
                  FROM qiita.filepath
@@ -791,8 +787,8 @@ def _add_file(self, filename, filetype, data_type=None, conn_handler=None):
         data_type : str, optional
         conn_handler : SQLConnectionHandler object, optional
         """
-        conn_handler = conn_handler if conn_handler is not None \
-            else SQLConnectionHandler()
+        conn_handler = SQLConnectionHandler() \
+
 
         filetype_id = convert_to_id(filetype, 'filepath_type', conn_handler)
         _, mp = get_mountpoint('analysis', conn_handler)[0]

qiita_db/base.py

@@ -132,8 +132,7 @@ def _check_id(self, id_, conn_handler=None):
         """
         self._check_subclass()
 
-        conn_handler = (conn_handler if conn_handler is not None
-                        else SQLConnectionHandler())
+        conn_handler = SQLConnectionHandler()
 
         return conn_handler.execute_fetchone(
             "SELECT EXISTS(SELECT * FROM qiita.{0} WHERE "
@@ -265,8 +264,8 @@ def check_status(self, status, exclude=False, conn_handler=None):
         self._check_subclass()
 
         # Get all available statuses
-        conn_handler = (conn_handler if conn_handler is not None
-                        else SQLConnectionHandler())
+        conn_handler = SQLConnectionHandler()
+
         statuses = [x[0] for x in conn_handler.execute_fetchall(
             "SELECT DISTINCT status FROM qiita.{0}_status".format(self._table),
             (self._id, ))]

qiita_db/data.py

@@ -147,7 +147,7 @@ def add_filepaths(self, filepaths, conn_handler=None):
 
         # Check if the connection handler has been provided. Create a new
         # one if not.
-        conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+        conn_handler = SQLConnectionHandler()
 
         # Update the status of the current object
         self._set_link_filepaths_status("linking")
@@ -478,7 +478,7 @@ def _is_preprocessed(self, conn_handler=None):
         bool
             whether the RawData has been preprocessed or not
         """
-        conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+        conn_handler = SQLConnectionHandler()
         return conn_handler.execute_fetchone(
             "SELECT EXISTS(SELECT * FROM qiita.prep_template_preprocessed_data"
             " PTPD JOIN qiita.prep_template PT ON PT.prep_template_id = "

qiita_db/metadata_template/base_metadata_template.py

@@ -492,8 +492,9 @@ class MetadataTemplate(QiitaObject):
     def _check_id(self, id_, conn_handler=None):
         r"""Checks that the MetadataTemplate id_ exists on the database"""
         self._check_subclass()
-        conn_handler = (conn_handler if conn_handler is not None
-                        else SQLConnectionHandler())
+
+        conn_handler = SQLConnectionHandler()
+
         return conn_handler.execute_fetchone(
             "SELECT EXISTS(SELECT * FROM qiita.{0} WHERE "
             "{1}=%s)".format(self._table, self._id_column),
@@ -1032,7 +1033,7 @@ def add_filepath(self, filepath, conn_handler=None, fp_id=None):
 
         # Check if the connection handler has been provided. Create a new
         # one if not.
-        conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+        conn_handler = SQLConnectionHandler()
         fp_id = self._fp_id if fp_id is None else fp_id
 
         try:
@@ -1056,7 +1057,7 @@ def get_filepaths(self, conn_handler=None):
 
         # Check if the connection handler has been provided. Create a new
         # one if not.
-        conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+        conn_handler = SQLConnectionHandler()
 
         try:
             filepath_ids = conn_handler.execute_fetchall(

qiita_db/parameters.py

@@ -133,8 +133,8 @@ def _check_id(self, id_, conn_handler=None):
         """
         self._check_subclass()
 
-        conn_handler = (conn_handler if conn_handler is not None
-                        else SQLConnectionHandler())
+        conn_handler = SQLConnectionHandler()
+
         return conn_handler.execute_fetchone(
             "SELECT EXISTS(SELECT * FROM qiita.{0} WHERE {1} = %s)".format(
                 self._table, self._column_id),

qiita_db/user.py

@@ -82,8 +82,8 @@ def _check_id(self, id_, conn_handler=None):
         """
         self._check_subclass()
 
-        conn_handler = (conn_handler if conn_handler is not None
-                        else SQLConnectionHandler())
+        conn_handler = SQLConnectionHandler()
+
         return conn_handler.execute_fetchone(
             "SELECT EXISTS(SELECT * FROM qiita.qiita_user WHERE "
             "email = %s)", (id_, ))[0]
@@ -454,7 +454,7 @@ def _change_pass(self, newpass, conn_handler=None):
 
         sql = ("UPDATE qiita.{0} SET password=%s, pass_reset_code=NULL WHERE "
                "email = %s".format(self._table))
-        conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+        conn_handler = SQLConnectionHandler()
         conn_handler.execute(sql, (hash_password(newpass), self._id))
 
 

qiita_db/util.py

@@ -341,7 +341,7 @@ def get_table_cols(table, conn_handler=None):
     list of str
         The column headers of `table`
     """
-    conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+    conn_handler = SQLConnectionHandler()
     headers = conn_handler.execute_fetchall(
         "SELECT column_name FROM information_schema.columns WHERE "
         "table_name=%s AND table_schema='qiita'", (table, ))
@@ -363,7 +363,7 @@ def get_table_cols_w_type(table, conn_handler=None):
     list of tuples of (str, str)
         The column headers and data type of `table`
     """
-    conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+    conn_handler = SQLConnectionHandler()
     return conn_handler.execute_fetchall(
         "SELECT column_name, data_type FROM information_schema.columns WHERE "
         "table_name=%s", (table,))
@@ -412,8 +412,8 @@ def get_db_files_base_dir(conn_handler=None):
     str
         The path to the base directory of all db files
     """
-    conn_handler = (conn_handler if conn_handler is not None
-                    else SQLConnectionHandler())
+    conn_handler = SQLConnectionHandler()
+
     return conn_handler.execute_fetchone(
         "SELECT base_data_dir FROM settings")[0]
 
@@ -426,8 +426,8 @@ def get_work_base_dir(conn_handler=None):
     str
         The path to the base directory of all db files
     """
-    conn_handler = (conn_handler if conn_handler is not None
-                    else SQLConnectionHandler())
+    conn_handler = SQLConnectionHandler()
+
     return conn_handler.execute_fetchone(
         "SELECT base_work_dir FROM settings")[0]
 
@@ -555,8 +555,8 @@ def get_mountpoint(mount_type, conn_handler=None, retrieve_all=False):
     list
         List of tuple, where: [(id_mountpoint, filepath_of_mountpoint)]
     """
-    conn_handler = (conn_handler if conn_handler is not None
-                    else SQLConnectionHandler())
+    conn_handler = SQLConnectionHandler()
+
     if retrieve_all:
         result = conn_handler.execute_fetchall(
             "SELECT data_directory_id, mountpoint, subdirectory FROM "
@@ -586,7 +586,7 @@ def get_mountpoint_path_by_id(mount_id, conn_handler=None):
     str
         The mountpoint path
     """
-    conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+    conn_handler = SQLConnectionHandler()
     mountpoint, subdirectory = conn_handler.execute_fetchone(
         """SELECT mountpoint, subdirectory FROM qiita.data_directory
            WHERE data_directory_id=%s""", (mount_id,))
@@ -676,7 +676,7 @@ def purge_filepaths(conn_handler=None):
     conn_handler : SQLConnectionHandler, optional
         The connection handler object connected to the DB
     """
-    conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+    conn_handler = SQLConnectionHandler()
 
     # Get all the (table, column) pairs that reference to the filepath table
     # Code adapted from http://stackoverflow.com/q/5347050/3746629
@@ -733,7 +733,7 @@ def move_filepaths_to_upload_folder(study_id, filepaths, conn_handler=None):
     conn_handler : SQLConnectionHandler, optional
         The connection handler object connected to the DB
     """
-    conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+    conn_handler = SQLConnectionHandler()
     uploads_fp = join(get_mountpoint("uploads")[0][1], str(study_id))
 
     # We can now go over and remove all the filepaths
@@ -848,7 +848,7 @@ def convert_to_id(value, table, conn_handler=None):
     IncompetentQiitaDeveloperError
         The passed string has no associated id
     """
-    conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+    conn_handler = SQLConnectionHandler()
     sql = "SELECT {0}_id FROM qiita.{0} WHERE {0} = %s".format(table)
     _id = conn_handler.execute_fetchone(sql, (value, ))
     if _id is None:
@@ -879,7 +879,7 @@ def convert_from_id(value, table, conn_handler=None):
     ValueError
         The passed id has no associated string
     """
-    conn_handler = conn_handler if conn_handler else SQLConnectionHandler()
+    conn_handler = SQLConnectionHandler()
     string = conn_handler.execute_fetchone(
         "SELECT {0} FROM qiita.{0} WHERE {0}_id = %s".format(table),
         (value, ))
@@ -989,8 +989,9 @@ def get_environmental_packages(conn_handler=None):
         environmental package name and the second string is the table where
         the metadata for the environmental package is stored
     """
-    conn = conn_handler if conn_handler else SQLConnectionHandler()
-    return conn.execute_fetchall("SELECT * FROM qiita.environmental_package")
+    conn_handler = SQLConnectionHandler()
+    return conn_handler.execute_fetchall(
+        "SELECT * FROM qiita.environmental_package")
 
 
 def get_timeseries_types(conn_handler=None):
@@ -1007,8 +1008,8 @@ def get_timeseries_types(conn_handler=None):
         The available timeseries types. Each timeseries type is defined by the
         tuple (timeseries_id, timeseries_type, intervention_type)
     """
-    conn = conn_handler if conn_handler else SQLConnectionHandler()
-    return conn.execute_fetchall(
+    conn_handler = SQLConnectionHandler()
+    return conn_handler.execute_fetchall(
         "SELECT * FROM qiita.timeseries_type ORDER BY timeseries_type_id")