changeset 13:c1d4f14dc768 draft

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

Binary file data_manager/.tmp.py.swp has changed

--- /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)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/metanetx_chem_prop_fetcher.xml	Wed Mar 09 14:22:54 2022 +0000
@@ -0,0 +1,50 @@
+<tool id="metanetx_chem_prop_fetcher" name="Metanetx Chem Prop data manager" tool_type="manage_data" profile="18.09" version="0.0.1">
+    <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'
+            #if $input_cond.input_select == "latest"
+                --version latest
+            #else
+                --version '$input_cond.version_id'
+            #end if
+            --out-file '$out_file'
+    ]]></command>
+    <inputs>
+        <conditional name="input_cond">
+            <param name="input_select" type="select" label="Select a version to download">
+                <option value="latest">Download latest</option>
+                <option value="version">Choose version</option>
+            </param>
+            <when value="version">
+                <param name="version_id" type="text" label="Version ID to download" value="">
+                    <validator type="empty_field" message="Version ID is required"/>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+Download InChI from Metanetx
+============================
+
+Get InChI value of compound in chem_prop.tsv file available from Metanetx
+
+Version
+----------
+0.0.1
+
+License
+-------
+
+`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
+
+    ]]></help>
+</tool>

--- a/data_manager_conf.xml	Thu Feb 24 13:09:32 2022 +0000
+++ b/data_manager_conf.xml	Wed Mar 09 14:22:54 2022 +0000
@@ -16,4 +16,13 @@
             </output>
         </data_table>
     </data_manager>
+    <data_manager tool_file="data_manager/metanetx_chem_prop_fetcher.xml" id="metanetx_chem_prop_fetcher">
+        <data_table name="metanetx_chem_prop">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="inchi" />
+            </output>
+        </data_table>
+    </data_manager>
 </data_managers>