# HG changeset patch
# User tduigou
# Date 1761546387 0
# Node ID 7a57f54c130f3e330dda7abde66477b5329f50c2
# Parent  6bcd8f09158d16d2347a97b236ea860d9f6d93a4
planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit dda8b49daae051df39f4a58d5c0d81fbc393cdf4

diff -r 6bcd8f09158d -r 7a57f54c130f get_infos.py
--- a/get_infos.py	Tue Apr 01 10:00:36 2025 +0000
+++ b/get_infos.py	Mon Oct 27 06:26:27 2025 +0000
@@ -1,7 +1,6 @@
 from argparse import ArgumentParser
 from libsbml import readSBMLFromFile
-from taxonid import get_taxonid
-from requests import get as r_get
+from requests import RequestException, get as r_get
 
 
 def get_biomass_rxn(sbml_doc):
@@ -62,12 +61,32 @@
             return organism
     except Exception as e:
         print(f"Error querying BiGG: {e}")
-    return None
+    return -1
+
 
-def get_taxon_id(input_name):
+def get_taxonid(organism_name: str) -> str:
+    """Query NCBI Taxonomy for a given organism name and return its Taxon ID."""
+    url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+    params = {
+        "db": "taxonomy",
+        "term": organism_name,
+        "retmode": "json"
+    }
+    try:
+        response = r_get(url, params=params, timeout=10)
+        response.raise_for_status()
+        data = response.json()
+        ids = data.get("esearchresult", {}).get("idlist", [])
+        return ids[0] if ids else -1
+    except RequestException as e:
+        print(f"Error querying NCBI for '{organism_name}': {e}")
+        return -1
+
+
+def get_taxon_id(input_name: str) -> str:
     """Try BiGG model name first, then NCBI directly."""
     print(f"Trying input: {input_name}")
-    
+
     # Try resolving as a BiGG model
     organism = get_organism_from_bigg_model(input_name)
     if organism:
diff -r 6bcd8f09158d -r 7a57f54c130f get_sbml_model.xml
--- a/get_sbml_model.xml	Tue Apr 01 10:00:36 2025 +0000
+++ b/get_sbml_model.xml	Mon Oct 27 06:26:27 2025 +0000
@@ -1,11 +1,10 @@
-<tool id="get_sbml_model" name="Pick SBML Model" version="0.4.0" profile="21.09" license="MIT">
+<tool id="get_sbml_model" name="Pick SBML Model" version="0.4.1" profile="21.09" license="MIT">
     <description>Get an SBML model (BiGG)</description>
     <requirements>
         <requirement type="package" version="7.81.0">curl</requirement>
         <requirement type="package" version="1.11">gzip</requirement>
         <requirement type="package" version="5.19.2">python-libsbml</requirement>
         <requirement type="package" version="2.31">requests</requirement>
-        <requirement type="package" version="0.1.1">taxonid</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #import re
@@ -36,11 +35,16 @@
                 <option value="from_history">Select file from the History</option>
             </param>
             <when value="from_history">
-                <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
+                <param name="input_file" type="data" format="sbml,xml" label="SBML model"
+                    help="An SBML file is expected" />
                 <section name="adv" title="Advanced Options" expanded="false">
-                    <param name="biomassid" type="text" label="Biomass reaction ID" help="Biomass reaction ID" optional="True"/>
-                    <param name="taxonid" type="text" label="Taxonomy ID" help="Taxonomy ID" optional="True"/>
-                    <param argument="--standalone" type="boolean" truevalue="--standalone" falsevalue="" checked="false" label="Standalone mode" help="If true, do not retrieve taxonomy ID from Internet" />
+                    <param name="biomassid" type="text" label="Biomass reaction ID"
+                        help="Biomass reaction ID" optional="True" />
+                    <param name="taxonid" type="text" label="Taxonomy ID" help="Taxonomy ID"
+                        optional="True" />
+                    <param argument="--standalone" type="boolean" truevalue="--standalone"
+                        falsevalue="" checked="false" label="Standalone mode"
+                        help="If true, do not retrieve taxonomy ID from Internet" />
                 </section>
             </when>
             <when value="from_bigg">
@@ -55,23 +59,27 @@
                     <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
                     <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
                     <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
-                    <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
+                    <option value="iML1515" selected="true">Escherichia coli str. K-12 substr.
+                        MG1655 (iML1515)</option>
                     <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
                     <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
-                    <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
+                    <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655
+                        (e_coli_core)</option>
                     <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
                     <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
                     <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
                     <option value="Recon3D">Homo sapiens (Recon3D)</option>
                     <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
                     <option value="RECON1">Homo sapiens (RECON1)</option>
-                    <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
+                    <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578
+                        (iYL1228)</option>
                     <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
                     <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
                     <option value="iMM1415">Mus musculus (iMM1415)</option>
                     <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
                     <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
-                    <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
+                    <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1
+                        (iLB1027_lipid)</option>
                     <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
                     <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
                     <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
@@ -81,17 +89,21 @@
                     <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
                     <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
                     <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
-                    <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
+                    <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium
+                        str. LT2 (STM_v1_0)</option>
                     <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
                     <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
-                    <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
+                    <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516
+                        (iYS854)</option>
                     <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
                     <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
                     <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
                     <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
                     <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
-                    <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
-                    <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
+                    <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c
+                        (iIS312_Trypomastigote)</option>
+                    <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c
+                        (iIS312_Epimastigote)</option>
                     <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
                 </param>
             </when>
@@ -113,10 +125,12 @@
         <data name="taxid_history" format="tsv" label="${cond_src.input_file.name} (taxon id)">
             <filter>cond_src['from_src'] == 'from_history'</filter>
         </data>
-        <data name="compartments_history" format="tsv" label="${cond_src.input_file.name} (compartments)">
+        <data name="compartments_history" format="tsv"
+            label="${cond_src.input_file.name} (compartments)">
             <filter>cond_src['from_src'] == 'from_history'</filter>
         </data>
-        <data name="biomass_history" format="tsv" label="${cond_src.input_file.name} (biomass reactions)">
+        <data name="biomass_history" format="tsv"
+            label="${cond_src.input_file.name} (biomass reactions)">
             <filter>cond_src['from_src'] == 'from_history'</filter>
         </data>
     </outputs>
@@ -205,15 +219,15 @@
 Download the selected SBML model fromg BiGG database or get statistics from local SBML model.
     ]]></help>
     <creator>
-        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+        <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/},
+            author = {Joan Hérisson},
+            title = {{get_sbml_model}},
+            url = {https://github.com/brsynth/},
             }
         </citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file