--- a/LICENSE	Mon Apr 03 09:18:22 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-MIT License
-
-Copyright (c) 2020 Jean-Loup Faulon's group & INRA
-Copyright (c) 2020 University of Evry / Paris-Saclay
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

--- a/README.md	Mon Apr 03 09:18:22 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-# get_sbml_model - Pick an SBML model among a list
-
-## How to run get_sbml_model wrapper tests
-
-In order to execute tests on get_sbml_model wrapper, you need to:
-
-  - Connect to your galaxy instance in interactive mode:
-
-  ```bash
-    docker exec -it -u root galaxy_galaxy_1 bash
-  ```
-  - Copy all the contents of `test-data` folder into your own test-data directory which is located in your local galaxy instance : `/galaxy/test-data`. It contains all the input files and expected output files needed for the tests.
-
-  - Install Planemo:
-  You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html
-  Note that they recommand to install Planemo by setting up a virtual environment:
-
-  ```bash
-  python3 -m venv planemo
-  . planemo/bin/activate
-  pip install -U planemo
-  ```
-
-  - run the tests:
-
-  ```bash
-  planemo test tools/synbiocad-galaxy-wrappers/get_sbml_model/wrap.xml
-  ```
-
-  IMPORTANT: Maybe you will need to remove CONDA from your PATH for the command `planemo test` to run correctly. To do that, you can edit this file `~/.bashrc`, comment this line `PATH="/root/anaconda3/bin:$PATH"` and save changes.
-
-  Planemo will output an html test summary `tool_test_output.html`.
\ No newline at end of file

--- a/get_infos.py	Mon Apr 03 09:18:22 2023 +0000
+++ b/get_infos.py	Mon Apr 24 14:49:53 2023 +0000
@@ -2,6 +2,7 @@
 from libsbml import (
     readSBMLFromFile
 )
+from requests import get as r_get
 
 
 def entry_point():
@@ -21,6 +22,16 @@
         type=str,
         help='Path to store biomass reaction ID'
     )
+    parser.add_argument(
+        '--hostid',
+        type=str,
+        help='Extended name of the host organism'
+    )
+    parser.add_argument(
+        '--taxid',
+        type=str,
+        help='Path to store host taxonomy ID'
+    )
     params = parser.parse_args()
 
     sbml_doc = readSBMLFromFile(params.infile)
@@ -40,5 +51,34 @@
                 if 'biomass' in rxn.getId().lower():
                     f.write(f'{rxn.getId()}\n')
 
+    if params.taxid:
+        # Extended Name
+        server = 'http://bigg.ucsd.edu/api/v2/models/'
+        ext = params.hostid
+        r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
+        if not r.ok:
+            print(f"Warning: unable to retrieve host name for id {params.hostid}")
+        else:
+            try:
+                hostname = r.json()["organism"]
+            except KeyError:
+                print(f"*** Error: unable to retrieve host name for id {params.hostid}")
+                return -1
+        # TAXON ID
+        server = 'https://rest.ensembl.org'
+        ext = f'/taxonomy/id/{hostname}?'
+        r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
+        if not r.ok:
+            print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+        else:
+            try:
+                taxid = r.json()["parent"]["id"]
+            except KeyError:
+                print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+            with open(params.taxid, 'w') as f:
+                f.write('#ID\n')
+                f.write(f'{taxid}\n')
+
+
 if __name__ == "__main__":
     entry_point()
\ No newline at end of file

--- a/get_sbml_model.xml	Mon Apr 03 09:18:22 2023 +0000
+++ b/get_sbml_model.xml	Mon Apr 24 14:49:53 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.2" profile="19.09" license="MIT">
+<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT">
     <description>Get an SBML model (BiGG)</description>
     <requirements>
         <requirement type="package" version="7.81.0">curl</requirement>
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
         | gunzip > '$model';
-        python '$__tool_directory__/'get_infos.py '$model' --comp '$compartments' --biomass '$biomass'
+        python '$__tool_directory__/'get_infos.py '$model' --hostid '$input' --comp '$compartments' --biomass '$biomass' --taxid '$taxid'
     ]]></command>
     <inputs>
         <param name="input" type="select" label="Strain">
@@ -63,6 +63,7 @@
     </inputs>
     <outputs>
         <data name="model" format="sbml" label="${input}" />
+        <data name="taxid" format="tsv" label="${input} (taxon id)" />
         <data name="compartments" format="tsv" label="${input} (compartments)" />
         <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
     </outputs>
@@ -71,7 +72,8 @@
         <!-- test 1: check if identical outputs are produced with iML1515 model input  -->
             <param name="input" value="iML1515" />
             <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
-            <output name="comp" md5="e93a875a2d8efc10a880ae3ac0018236"/>
+            <output name="taxid" md5="ec29688652dd49becf7be2a6c2469287"/>
+            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
             <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
         </test>
     </tests>
@@ -84,4 +86,13 @@
     <creator>
         <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
     </creator>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{get_sbml_model
+                author = {Joan Hérisson},
+                title = {{get_sbml_model}},
+                url = {https://github.com/brsynth/},
+            }
+        </citation>
+    </citations>
 </tool>