Merge pull request #29 from mad-lab-fau/28-clarify-number-of-biomarke…

…r-samples-prompt

28 clarify number of biomarker samples prompt

carwatch/labels/label_generator.py

@@ -276,7 +276,7 @@ def _generate_label_tex(self, barcode_id: int):
             # center text in label
             label_head = "\\genericlabel\n\\begin{center}\n\\begin{tabular}"
             label_foot = "\\end{tabular}\n\\end{center}\n\n"
-        if self.study.has_evening_sample and all([sample == self.study.num_samples - 1]):
+        if self.study.has_evening_sample and all([sample == self.study.num_samples]):
             # if last sample of the day is evening sample, it is marked with "E"
             sample_name = "E"
         if self.add_name:

carwatch/qr_codes/study_qr_generator.py

@@ -128,23 +128,18 @@ def _save_qr_img(self, qr_img):
         qr_img.save(img_location)
 
     def _sanitize_distances(self, saliva_distances: Union[int, Sequence[int]]) -> Sequence[int]:
-        # required number of saliva distances
-        num_morning_samples = self.study.num_samples
-        if self.study.has_evening_sample:
-            # evening sample counts into total number of distances
-            num_morning_samples = num_morning_samples - 1
         if isinstance(saliva_distances, int):
-            return [saliva_distances] * (num_morning_samples - 1)
+            return [saliva_distances] * (self.study.num_samples - 1)
         if isinstance(saliva_distances, list):
             # all elements are ints
             if all(isinstance(dist, int) for dist in saliva_distances):
                 # length is correct
-                if len(saliva_distances) == num_morning_samples - 1:
+                if len(saliva_distances) == self.study.num_samples - 1:
                     return saliva_distances
                 raise ValueError(
                     f"Incorrect number of saliva distances provided! "
-                    f"Needs to be {num_morning_samples - 1}, as "
-                    f"{num_morning_samples} morning samples will be taken."
+                    f"Needs to be {self.study.num_samples - 1}, as "
+                    f"{self.study.num_samples} samples will be taken throughout the day."
                 )
             raise ValueError("Invalid data detected in saliva distances! All values need to be integers!")
         raise ValueError("Saliva distances data type is invalid! Needs to be int or list of ints.")

carwatch/scripts/prepare_study.py

@@ -89,9 +89,9 @@
 @click.option(
     "--num-samples",
     required=True,
-    prompt="Number of biomarker samples [per day]",
+    prompt="Number of biomarker samples [during the day, WITHOUT evening sample]",
     type=int,
-    help="The daily number of biomarker samples taken from every participant.",
+    help="The daily number of biomarker samples taken throughout the day from every participant. This number does not include the evening sample.",
 )
 @click.option(
     "--sample_prefix",
@@ -117,9 +117,9 @@
 )
 @click.option(
     "--has-evening-sample",
-    prompt="Evening sample taken?",
+    prompt="Additional evening sample taken?",
     is_flag=True,
-    help="Whether a biomarker sample is taken in the evening.",
+    help="Whether an additional biomarker sample is taken in the evening.",
     cls=NumericChoice,
     chosen_number="study_type",
     option_map=EVENING_OPTION,

carwatch/utils/study.py

@@ -35,7 +35,7 @@ def __init__(
         num_days: int
             Number of days the study will be conducted
         num_samples: int
-            *Total* number of biomarker samples per day (including a potential evening sample!)
+            Number of biomarker samples per day (*excluding* a potential evening sample!)
         num_subjects: int, optional
             Number of subjects in the study
         subject_path: str or :class:`~pathlib.Path`, optional
@@ -46,7 +46,7 @@ def __init__(
         subject_prefix: str, optional
             Add prefix to participant number (e.g., "VP_")
         has_evening_sample: bool, optional
-            Whether a biomarker sample in the evening is also collected, default is ``False``
+            Whether an *additional* biomarker sample in the evening is collected, default is ``False``
         sample_prefix: str, optional
             Abbreviation of the type of sample taken, default is ``'S'`` for 'Saliva'
         start_sample_from_zero: bool, optional
@@ -180,4 +180,7 @@ def sample_indices(self):
             list of sample indices
 
         """
-        return list(range(0, self.num_samples))
+        if self.has_evening_sample:
+            return list(range(0, self.num_samples + 1))
+        else:
+            return list(range(0, self.num_samples))