# HG changeset patch
# User ggricourt
# Date 1646839087 0
# Node ID 8e8a9e51f1d7b2fd7e8982d720c675d48b827d3b
# Parent  c1d4f14dc76872162846ab74bcda7c56eb964bf0
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 7db54c0555a12ecb8b3f756032228c54fe028e0a-dirty"

diff -r c1d4f14dc768 -r 8e8a9e51f1d7 data_manager/.tmp.py.swp
Binary file data_manager/.tmp.py.swp has changed
diff -r c1d4f14dc768 -r 8e8a9e51f1d7 data_manager/metanetx_chem_prop_fetcher.py
--- a/data_manager/metanetx_chem_prop_fetcher.py	Wed Mar 09 14:22:54 2022 +0000
+++ b/data_manager/metanetx_chem_prop_fetcher.py	Wed Mar 09 15:18:07 2022 +0000
@@ -4,7 +4,7 @@
 import shutil
 import sys
 import tempfile
-import pandas as pd
+# import pandas as pd
 try:
     # For Python 3.0 and later
     from urllib.request import Request, urlopen
@@ -46,12 +46,28 @@
     shutil.copyfile(ftmp.name, path)
 
 
+# def records_chem_prop_pandas(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')
+
+
 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')
+    records = []
+    with open(path) as fid:
+        for ix, line in enumerate(fid):
+            if ix == 0:
+                continue
+            line = line.split("\t")
+            if line[7] != '':
+                records.append({
+                    "value": line[0],
+                    "name": "%s: %s (%s)" % (line[0], line[1], line[3]),
+                    "inchi": line[7],
+                })
+    return records
 
 
 if __name__ == "__main__":
diff -r c1d4f14dc768 -r 8e8a9e51f1d7 data_manager/metanetx_chem_prop_fetcher.xml
--- a/data_manager/metanetx_chem_prop_fetcher.xml	Wed Mar 09 14:22:54 2022 +0000
+++ b/data_manager/metanetx_chem_prop_fetcher.xml	Wed Mar 09 15:18:07 2022 +0000
@@ -2,7 +2,6 @@
     <description>Get InChI value of compound in chem_prop.tsv file available from Metanetx</description>
     <requirements>
         <requirement type="package" version="3.8">python</requirement>
-        <requirement type="package" version="1.4">pandas</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python '$__tool_directory__/metanetx_chem_prop_fetcher.py'