enforce str dtype for recording_filename/session_id/child_id

ChildProject/projects.py

@@ -36,6 +36,7 @@ class ChildProject:
             description="unique child ID -- unique within the experiment (Id could be repeated across experiments to refer to different children)",
             unique=True,
             required=True,
+            dtype="str",
         ),
         IndexColumn(
             name="child_dob",
@@ -127,6 +128,7 @@ class ChildProject:
             name="child_id",
             description="unique child ID -- unique within the experiment (Id could be repeated across experiments to refer to different children)",
             required=True,
+            dtype="str",
         ),
         IndexColumn(
             name="date_iso",
@@ -152,14 +154,17 @@ class ChildProject:
             required=True,
             filename=True,
             unique=True,
+            dtype="str",
         ),
         IndexColumn(
             name="duration",
             description="duration of the audio, in milliseconds",
             regex=r"([0-9]+)",
         ),
         IndexColumn(
-            name="session_id", description="identifier of the recording session."
+            name="session_id",
+            description="identifier of the recording session.",
+            dtype="str",
         ),
         IndexColumn(
             name="session_offset",
@@ -207,13 +212,15 @@ class ChildProject:
 
     PROJECT_FOLDERS = ["recordings", "annotations", "metadata", "doc", "scripts"]
 
-    def __init__(self, path: str):
+    def __init__(self, path: str, enforce_dtypes: bool = False):
         """Constructor
 
         :param path: path to the root of the dataset.
         :type path: str
         """
         self.path = path
+        self.enforce_dtypes = enforce_dtypes
+
         self.errors = []
         self.warnings = []
         self.children = None
@@ -272,7 +279,7 @@ def accumulate_metadata(
             if not os.path.exists(md):
                 continue
 
-            table = IndexTable(table, md, columns)
+            table = IndexTable(table, md, columns, enforce_dtypes=self.enforce_dtypes)
             dataframe = table.read()
 
             replaced_columns = (set(df.columns) & set(dataframe.columns)) - {
@@ -303,11 +310,13 @@ def read(self, verbose=False):
             "children",
             os.path.join(self.path, "metadata/children.csv"),
             self.CHILDREN_COLUMNS,
+            enforce_dtypes=self.enforce_dtypes
         )
         self.rt = IndexTable(
             "recordings",
             os.path.join(self.path, "metadata/recordings.csv"),
             self.RECORDINGS_COLUMNS,
+            enforce_dtypes=self.enforce_dtypes
         )
 
         self.children = self.ct.read()

ChildProject/tables.py

@@ -20,6 +20,7 @@ def __init__(
         datetime=None,
         function=None,
         choices=None,
+        dtype=None,
         unique=False,
         generated=False,
     ):
@@ -33,6 +34,7 @@ def __init__(
         self.choices = choices
         self.unique = unique
         self.generated = generated
+        self.dtype = dtype
 
     def __str__(self):
         return "IndexColumn(name = {})".format(self.name)
@@ -42,11 +44,12 @@ def __repr__(self):
 
 
 class IndexTable:
-    def __init__(self, name, path=None, columns=[]):
+    def __init__(self, name, path=None, columns=[],enforce_dtypes: bool = False):
         self.name = name
         self.path = path
         self.columns = columns
         self.df = None
+        self.enforce_dtypes = enforce_dtypes
 
     def read(self):
         pd_flags = {
@@ -74,7 +77,12 @@ def read(self):
             "index_col": False,
         }
 
-        self.df = pd.read_csv(self.path, **pd_flags)
+        if self.enforce_dtypes:
+            dtype = {column.name: column.dtype for column in self.columns if column.dtype}
+            self.df = pd.read_csv(self.path, dtype=dtype, **pd_flags)
+        else:
+            self.df = pd.read_csv(self.path, **pd_flags)
+
         self.df.index = self.df.index + 2
         return self.df
 

tests/test_projects.py

@@ -0,0 +1,14 @@
+from ChildProject.projects import ChildProject
+
+def test_enforce_dtypes():
+    project = ChildProject("examples/valid_raw_data", enforce_dtypes=True)
+    project.read()
+
+    assert project.recordings['child_id'].dtype.kind == 'O'
+    assert project.children['child_id'].dtype.kind == 'O'
+
+    project = ChildProject("examples/valid_raw_data", enforce_dtypes=False)
+    project.read()
+
+    assert project.recordings['child_id'].dtype.kind == 'i'
+    assert project.children['child_id'].dtype.kind == 'i'

tests/truth/aclew_metrics.csv

@@ -1,2 +1,2 @@
 child_id,voc_fem_ph,voc_dur_fem_ph,avg_voc_dur_fem,voc_chi_ph,voc_dur_chi_ph,avg_voc_dur_chi,wc_fem_ph,sc_fem_ph,pc_fem_ph,wc_adu_ph,sc_adu_ph,pc_adu_ph,cry_voc_chi_ph,cry_voc_dur_chi_ph,can_voc_chi_ph,can_voc_dur_chi_ph,avg_can_voc_dur_chi,non_can_voc_chi_ph,non_can_voc_dur_chi_ph,avg_non_can_voc_dur_chi,lp_n,cp_n,lp_dur,cp_dur,duration
-1,7200.0,720.0,0.1,18000.0,1800.0,0.1,7200.0,14400.0,28800.0,7200.0,14400.0,28800.0,0,0,9000.0,900.0,0.1,9000.0,900.0,0.1,1.0,0.5,1.0,0.5,4.0
+"1",7200.0,720.0,0.1,18000.0,1800.0,0.1,7200.0,14400.0,28800.0,7200.0,14400.0,28800.0,0,0,9000.0,900.0,0.1,9000.0,900.0,0.1,1.0,0.5,1.0,0.5,4.0

tests/truth/period_metrics.csv

@@ -1,13 +1,13 @@
 child_id,voc_fem_ph,voc_dur_fem_ph,avg_voc_dur_fem,voc_mal_ph,voc_dur_mal_ph,avg_voc_dur_mal,voc_chi_ph,voc_dur_chi_ph,avg_voc_dur_chi,voc_och_ph,voc_dur_och_ph,avg_voc_dur_och,duration,period
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,00:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,02:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,04:00:00
-1,720.0000100000007,720.0000100000007,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7199999,06:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,3600000,08:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,10:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,12:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,14:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,16:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,18:00:00
-1,720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,20:00:00
-1,720.0000100000007,720.0000100000007,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7199999,22:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,00:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,02:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,04:00:00
+"1",720.0000100000007,720.0000100000007,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7199999,06:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,3600000,08:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,10:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,12:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,14:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,16:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,18:00:00
+"1",720.0,720.0,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7200000,20:00:00
+"1",720.0000100000007,720.0000100000007,1.0,0.0,0.0,,0.0,0.0,,0.0,0.0,,7199999,22:00:00