chore(code): Refactor yml loading code

Fix for new paths and restructure to have the from_yml and to_tsv
functions in the same data loading file.
Improved path behavior to resolve any paths to absolutes before
loading.

01-scripts/data.py

@@ -4,19 +4,41 @@ import sys
 import load_yaml
 from pandas import DataFrame, read_csv
 
-DEFAULT_YAML_PATH = Path("../02-data/intermediate/relevant")
+DEFAULT_YAML_PATH = Path("02-data/processed/relevant")
 
 
-def load(yml_path: Path | str = DEFAULT_YAML_PATH) -> DataFrame:
-    studies = load_yaml.from_yml(yml_path)
-    tsv = load_yaml.to_tsv(studies)
+def to_tsv(studies: list[dict]) -> str:
+    if not studies:
+        return ""
+    tsv = ""
+    tab = "\t"
+    tsv += (
+        f"{tab.join(studies[0].keys())}{tab}"
+        f"{tab.join(studies[0]['observation'][0].keys())}\n"
+    )
+    for study in studies:
+        study_list = [str(val).replace("\n", "") for val in study.values()]
+        for obs in study["observation"]:
+            obs_list = [str(val).replace("\n", "") for val in obs.values()]
+            tsv += f"{tab.join(study_list)}{tab}{tab.join(obs_list)}\n"
+    return tsv
+
+
+def from_yml(yml_path: Path | str = DEFAULT_YAML_PATH) -> DataFrame:
+    yml_path = Path(yml_path).resolve()
+    studies = load_yaml.load(yml_path)
+    if not studies:
+        raise ValueError(f"No studies found in directory {yml_path.resolve()}")
+    tsv = to_tsv(studies)
     return read_csv(io.StringIO(tsv), sep="\t")
 
 
 if __name__ == "__main__":
     if len(sys.argv) == 2:
-        res = load(Path(sys.argv[1]))
+        res = from_yml(Path(sys.argv[1]))
     else:
-        res = load()
+        res = from_yml()
 
     print(res)
+    # print out tsv file instead
+    # print(to_tsv(load_yaml.load(DEFAULT_YAML_PATH)))

01-scripts/load_yaml.py

@@ -3,12 +3,10 @@ from typing import cast
 import yaml
 from pathlib import Path
 
-DEFAULT_YAML_PATH = Path("../02-data/intermediate/relevant")
-
 
 def _get_all_yml(path: Path) -> list:
     """Returns list of all yml files."""
-    return list(path.rglob(r"*.y*ml"))
+    return list(path.rglob(r"**/*.y*ml"))
 
 
 def _read_yml(path: Path) -> dict | None:
@@ -20,9 +18,7 @@ def _read_yml(path: Path) -> dict | None:
     return None
 
 
-def from_yml(
-    yml_path: Path | str = DEFAULT_YAML_PATH,
-) -> list[dict]:
+def load(yml_path: Path | str) -> list[dict]:
     """Main data process routine.
     Extracts all necessary data from yaml files returns it.
     """
@@ -35,25 +31,9 @@ def from_yml(
     return contents
 
 
-def to_tsv(studies: list[dict]) -> str:
-    tsv = ""
-    tab = "\t"
-    tsv += (
-        f"{tab.join(studies[0].keys())}{tab}"
-        f"{tab.join(studies[0]['observation'][0].keys())}\n"
-    )
-    for study in studies:
-        study_list = [str(val).replace("\n", "") for val in study.values()]
-        for obs in study["observation"]:
-            obs_list = [str(val).replace("\n", "") for val in obs.values()]
-            tsv += f"{tab.join(study_list)}{tab}{tab.join(obs_list)}\n"
-    return tsv
-
-
 if __name__ == "__main__":
     if len(sys.argv) == 2:
-        res = from_yml(Path(sys.argv[1]))
+        res = load(Path(sys.argv[1]))
+        print(res)
     else:
-        res = from_yml()
-
-    print(to_tsv(res))
+        print("Please provide path to yml files.")