diff med_environ.py @ 0:f82f266381be draft

planemo upload for repository https://github.com/jeremyfix/medenv commit 6068531bc50297a9c8f2c24e748d7d791fe5f2ba

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/med_environ.py	Thu Feb 15 20:01:29 2024 +0000
@@ -0,0 +1,107 @@
+# coding: utf-8
+
+# Standard imports
+import argparse
+import os
+import pathlib
+from datetime import datetime
+
+# External imports
+import medenv
+
+import pandas as pd
+
+
+def environment_observation(
+    row,
+    fetcher,
+    lat_key,
+    long_key,
+    depth_key,
+    date_key,
+    tol_spatial_coordinates,
+    verbose,
+):
+    lat0 = (
+        row[lat_key] - tol_spatial_coordinates / 2.0,
+        row[lat_key] + tol_spatial_coordinates / 2.0,
+    )
+    long0 = (
+        row[long_key] - tol_spatial_coordinates / 2.0,
+        row[long_key] + tol_spatial_coordinates / 2.0,
+    )
+    depth = row[depth_key]
+    date = datetime.strptime(row[date_key], "%Y-%m-%dT%H:%M:%SZ")
+
+    values, info_values = fetcher.get_values(date, (long0, lat0), depth)
+
+    if verbose:
+        print(
+            f"Was fetching for date={date}, long={long0}, lat={lat0},"
+            f"depth={depth} and got {values} at the coordinates {info_values}"
+        )
+    for fname, fvalue in values.items():
+        row[fname] = fvalue
+    return row
+
+
+def environment_dataset(args):
+    # Note: galaxy is given us, for boolean parameters, the string
+    # "true" or the string "false" that we need to convert to a bool
+    verbose = True if args.verbose == "true" else False
+
+    if args.keyfile is not None and os.path.exists(args.keyfile):
+        with open(args.keyfile, "r") as fh:
+            key_lines = fh.readlines()
+            cmems_username = key_lines[0].split(":")[1].strip()
+            cmems_password = key_lines[1].split(":")[1].strip()
+            os.environ["CMEMS_USERNAME"] = cmems_username
+            os.environ["CMEMS_PASSWORD"] = cmems_password
+
+    features = args.variables.split(",")
+    fetcher = medenv.Fetcher(features, reduction="mean")
+
+    # Loads the input dataset
+    df = pd.read_csv(args.datafile, sep="\t")
+    lat_key = df.columns[args.lat_key]
+    long_key = df.columns[args.long_key]
+    depth_key = df.columns[args.depth_key]
+    date_key = df.columns[args.date_key]
+    print(lat_key, long_key, depth_key, date_key)
+
+    df = df.apply(
+        environment_observation,
+        args=(
+            fetcher,
+            lat_key,
+            long_key,
+            depth_key,
+            date_key,
+            args.tol_spatial_coordinates,
+            verbose,
+        ),
+        axis=1,
+    )
+
+    df.to_csv(args.out_file, header=True, index=False, sep="\t")
+
+
+def __main__():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--datafile", type=pathlib.Path, required=True)
+    parser.add_argument("--out_file", type=pathlib.Path, required=True)
+    parser.add_argument("--lat_key", type=int, required=True)
+    parser.add_argument("--long_key", type=int, required=True)
+    parser.add_argument("--date_key", type=int, required=True)
+    parser.add_argument("--depth_key", type=int, required=True)
+    parser.add_argument("--variables", type=str, required=True)
+    parser.add_argument("--tol_spatial_coordinates", type=float, required=True)
+    parser.add_argument("--keyfile", type=pathlib.Path, default=None)
+    parser.add_argument("--verbose", type=str, default=False)
+    args = parser.parse_args()
+
+    environment_dataset(args)
+
+
+if __name__ == "__main__":
+    __main__()