base: data_set: Rewrite data_set using @dataclass

@dataclasses should be used to hold only data. Since dataset only
encapsulates data, re-writing it using a dataclass makes it more
readable and easier to follow.

1 files changed, 48 insertions, 38 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cc5a428c..e3a85ff6 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -17,7 +17,10 @@
 # at rwilliams@uthsc.edu and xzhou15@uthsc.edu
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
-
+from dataclasses import dataclass
+from dataclasses import field
+from dataclasses import InitVar
+from typing import Optional, Dict
 from db.call import fetchall, fetchone, fetch1
 from utility.logger import getLogger
 from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
@@ -74,11 +77,10 @@ def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_n
         return dataset_class(dataset_name, get_samplelist)
 
 
+@dataclass
 class DatasetType:
-
-    def __init__(self, redis_instance):
-        """Create a dictionary of samples where the value is set to Geno,
-Publish or ProbeSet. E.g.
+    """Create a dictionary of samples where the value is set to Geno,
+    Publish or ProbeSet. E.g.
 
         {'AD-cases-controls-MyersGeno': 'Geno',
          'AD-cases-controls-MyersPublish': 'Publish',
@@ -89,21 +91,28 @@ Publish or ProbeSet. E.g.
          'All Phenotypes': 'Publish',
          'B139_K_1206_M': 'ProbeSet',
          'B139_K_1206_R': 'ProbeSet' ...
-
+        }
         """
+    redis_instance: InitVar[Redis]
+    datasets: Optional[Dict] = field(init=False, default_factory=dict)
+    data: Optional[Dict] = field(init=False)
+
+    def __post_init__(self, redis_instance):
         self.redis_instance = redis_instance
-        self.datasets = {}
-        data = self.redis_instance.get("dataset_structure")
+        data = redis_instance.get("dataset_structure")
         if data:
             self.datasets = json.loads(data)
-        else:  # ZS: I don't think this should ever run unless Redis is emptied
+        else:
+            # ZS: I don't think this should ever run unless Redis is
+            # emptied
             try:
                 data = json.loads(requests.get(
-                    GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content)
-                for species in data['datasets']:
-                    for group in data['datasets'][species]:
-                        for dataset_type in data['datasets'][species][group]:
-                            for dataset in data['datasets'][species][group][dataset_type]:
+                    GN2_BASE_URL + "/api/v_pre1/gen_dropdown",
+                    timeout=5).content)
+                for _species in data['datasets']:
+                    for group in data['datasets'][_species]:
+                        for dataset_type in data['datasets'][_species][group]:
+                            for dataset in data['datasets'][_species][group][dataset_type]:
                                 short_dataset_name = dataset[1]
                                 if dataset_type == "Phenotypes":
                                     new_type = "Publish"
@@ -112,15 +121,15 @@ Publish or ProbeSet. E.g.
                                 else:
                                     new_type = "ProbeSet"
                                 self.datasets[short_dataset_name] = new_type
-            except:
+            except Exception:  # Do nothing
                 pass
-
-            self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+            self.redis_instance.set("dataset_structure",
+                                    json.dumps(self.datasets))
+        self.data = data
 
     def set_dataset_key(self, t, name):
-        """If name is not in the object's dataset dictionary, set it, and update
-        dataset_structure in Redis
-
+        """If name is not in the object's dataset dictionary, set it, and
+        update dataset_structure in Redis
         args:
           t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
              'other_pheno', 'geno'
@@ -128,19 +137,20 @@ Publish or ProbeSet. E.g.
 
         """
         sql_query_mapping = {
-            'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ +
-                          """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """),
-            'pheno': ("""SELECT InfoFiles.GN_AccesionId """ +
-                      """FROM InfoFiles, PublishFreeze, InbredSet """ +
-                      """WHERE InbredSet.Name = '{}' AND """ +
-                      """PublishFreeze.InbredSetId = InbredSet.Id AND """ +
-                      """InfoFiles.InfoPageName = PublishFreeze.Name"""),
-            'other_pheno': ("""SELECT PublishFreeze.Name """ +
-                            """FROM PublishFreeze, InbredSet """ +
-                            """WHERE InbredSet.Name = '{}' AND """ +
-                            """PublishFreeze.InbredSetId = InbredSet.Id"""),
-            'geno':  ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ +
-                      """GenoFreeze.Name = "{}" """)
+            'mrna_expr': ("SELECT ProbeSetFreeze.Id FROM "
+                          "ProbeSetFreeze WHERE "
+                          "ProbeSetFreeze.Name = \"%s\" "),
+            'pheno': ("SELECT InfoFiles.GN_AccesionId "
+                      "FROM InfoFiles, PublishFreeze, InbredSet "
+                      "WHERE InbredSet.Name = '%s' AND "
+                      "PublishFreeze.InbredSetId = InbredSet.Id AND "
+                      "InfoFiles.InfoPageName = PublishFreeze.Name"),
+            'other_pheno': ("SELECT PublishFreeze.Name "
+                            "FROM PublishFreeze, InbredSet "
+                            "WHERE InbredSet.Name = '%s' AND "
+                            "PublishFreeze.InbredSetId = InbredSet.Id"),
+            'geno':  ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
+                      "GenoFreeze.Name = \"%s\" ")
         }
 
         dataset_name_mapping = {
@@ -154,22 +164,22 @@ Publish or ProbeSet. E.g.
         if t in ['pheno', 'other_pheno']:
             group_name = name.replace("Publish", "")
 
-        results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone()
+        results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
         if results:
             self.datasets[name] = dataset_name_mapping[t]
             self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
             return True
-
         return None
 
     def __call__(self, name):
-
         if name not in self.datasets:
             for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
-                # This has side-effects, with the end result being a truth-y value
+                # This has side-effects, with the end result being a
+                # truth-y value
                 if(self.set_dataset_key(t, name)):
                     break
-        return self.datasets.get(name, None)  # Return None if name has not been set
+        # Return None if name has not been set
+        return self.datasets.get(name, None)
 
 
 # Do the intensive work at startup one time only