diff data_manager/metanetx_chem_prop_fetcher.py @ 13:c1d4f14dc768 draft

"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 7db54c0555a12ecb8b3f756032228c54fe028e0a-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/metanetx_chem_prop_fetcher.py	Wed Mar 09 14:22:54 2022 +0000
@@ -0,0 +1,86 @@
+import argparse
+import json
+import os
+import shutil
+import sys
+import tempfile
+import pandas as pd
+try:
+    # For Python 3.0 and later
+    from urllib.request import Request, urlopen
+except ImportError:
+    # Fall back to Python 2 imports
+    from urllib2 import Request, urlopen
+
+
+METANETX_URL = "https://www.metanetx.org/ftp/"
+
+
+def url_download(url, path):
+    try:
+        with urlopen(Request(url)) as fod:
+            with open(path, "wb") as dst:
+                while True:
+                    chunk = fod.read(2**10)
+                    if chunk:
+                        dst.write(chunk)
+                    else:
+                        break
+    except Exception as e:
+        sys.exit(str(e))
+
+
+def clean_metanetx_file(path):
+    ftmp = tempfile.NamedTemporaryFile()
+    isHeaderFound = False
+    with open(path) as fid, open(ftmp.name, 'w') as fod:
+        for line in fid:
+            if line.startswith("#"):
+                last_line = line
+            else:
+                if not isHeaderFound:
+                    last_line = last_line.replace("#", "")
+                    fod.write(last_line)
+                    isHeaderFound = True
+                fod.write(line)
+    shutil.copyfile(ftmp.name, path)
+
+
+def records_chem_prop(path):
+    df = pd.read_csv(path, sep="\t")
+    df["name"] = df.apply(lambda x: "%s: %s (%s)" % (x["ID"], x["name"], x["formula"]), axis=1)
+    df.drop(columns=["reference", "formula", "charge", "mass", "InChIKey", "SMILES"], inplace=True)
+    df.rename(columns={"ID": "value", "InChI": "inchi"})
+    return df.to_dict('records')
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    pinput = parser.add_mutually_exclusive_group(required=True)
+    pinput.add_argument("--version", help="Version to download")
+    parser.add_argument("--out-file", help="JSON output file")
+    args = parser.parse_args()
+
+    # Init.
+    data_manager_json = {"data_tables": {}}
+    with open(args.out_file) as fh:
+        params = json.load(fh)
+
+    workdir = params["output_data"][0]["extra_files_path"]
+    os.makedirs(workdir)
+
+    # Load models and models metadata.
+    ftmp = tempfile.NamedTemporaryFile()
+    url = '/'.join([METANETX_URL, args.version, 'chem_prop.tsv'])
+    url_download(url, ftmp.name)
+
+    # Clean header
+    clean_metanetx_file(ftmp.name)
+
+    # Select records.
+    records = records_chem_prop(ftmp.name)
+
+    # Write data.
+    data_manager_json["data_tables"]["metanetx_chem_prop"] = records
+    with open(args.out_file, "w") as fh:
+        json.dump(data_manager_json, fh, sort_keys=True)