Split baseline data to participants.

And some csv I/O settings.

Snakefile

@@ -405,7 +405,7 @@ for provider in config["ALL_CLEANING_OVERALL"]["PROVIDERS"].keys():
 
 # Demographic features
 files_to_compute.extend(expand("data/raw/baseline_merged.csv"))
-#files_to_compute.extend(expand("data/raw/{pid}/participant_baseline_raw.csv", pid=config["PIDS"]))
+files_to_compute.extend(expand("data/raw/{pid}/participant_baseline_raw.csv", pid=config["PIDS"]))
 
 rule all:
     input:

rules/models.smk

@@ -6,3 +6,11 @@ rule merge_baseline_data:
     script:
         "../src/data/merge_baseline_data.py"
 
+rule download_baseline_data:
+    input:
+        participant_file = "data/external/participant_files/{pid}.yaml",
+        data = "data/raw/baseline_merged.csv"
+    output:
+        "data/raw/{pid}/participant_baseline_raw.csv"
+    script:
+        "../src/data/download_baseline_data.py"

src/data/download_baseline_data.py

@@ -0,0 +1,14 @@
+import pandas as pd
+import yaml
+
+filename = snakemake.input["data"]
+baseline = pd.read_csv(filename)
+
+with open(snakemake.input["participant_file"], "r") as file:
+    participant = yaml.safe_load(file)
+
+username = participant["PHONE"]["LABEL"]
+
+baseline[baseline["username"] == username].to_csv(snakemake.output[0],
+                                                  index=False,
+                                                  encoding="utf-8",)

src/data/merge_baseline_data.py

@@ -11,7 +11,11 @@ filenames = snakemake.input["data"]
 baseline_dfs = []
 
 for fn in filenames:
-    baseline_dfs.append(pd.read_csv(fn))
+    baseline_dfs.append(pd.read_csv(fn,
+                                    parse_dates=["Geboortedatum"],
+                                    infer_datetime_format=True,
+                                    cache_dates=True,
+                                    ))
 
 baseline = (
     pd.concat(baseline_dfs, join="inner")
@@ -22,8 +26,9 @@ baseline = (
 baseline.rename(columns=VARIABLES_TO_TRANSLATE, copy=False, inplace=True)
 now = pd.Timestamp("now")
 baseline = baseline.assign(
-    date_of_birth=lambda x: pd.to_datetime(x.date_of_birth),
     age=lambda x: (now - x.date_of_birth).dt.days / 365.25245,
 )
 
-baseline.to_csv(snakemake.output[0])
+baseline.to_csv(snakemake.output[0],
+                index=False,
+                encoding="utf-8",)