fix load from file

brsynth · Sep 1, 2023 · 4cffff2 · 4cffff2
1 parent 3412c99
commit 4cffff2
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Showing 2 changed files with 59 additions and 35 deletions.
diff --git a/tools/get_sbml_model/get_infos.py b/tools/get_sbml_model/get_infos.py
@@ -12,6 +12,12 @@ def entry_point():
         type=str,
         help='SBML input file (xml)'
     )
+    # argument to tag file from BiGG
+    parser.add_argument(
+        '--bigg',
+        action='store_true',
+        help='Tag file from BiGG'
+    )
     parser.add_argument(
         '--comp',
         type=str,
@@ -52,33 +58,41 @@ def entry_point():
                     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"Warning: unable to retrieve host name for id {params.hostid}")
-                hostname = ''
-        if not hostname:
-            taxid = ''
-        else:
-            # TAXON ID
-            server = 'https://rest.ensembl.org'
-            ext = f'/taxonomy/id/{hostname}?'
+        hostname = ''
+
+        # Model from BiGG
+        if params.bigg:
+            # 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 taxonomy ID for host organism {hostname}")
+                print(f"Warning: unable to retrieve host name for id {params.hostid}")
             else:
                 try:
-                    taxid = r.json()["id"]
+                    hostname = r.json()["organism"]
                 except KeyError:
+                    print(f"Warning: unable to retrieve host name for id {params.hostid}")
+            if not hostname:
+                taxid = ''
+            else:
+                # 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}")
-                    taxid = ''
+                else:
+                    try:
+                        taxid = r.json()["id"]
+                    except KeyError:
+                        print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
+                        taxid = ''
+
+        # Model from user
+        else:
+            taxid = params.hostid
+
         with open(params.taxid, 'w') as f:
             f.write('#ID\n')
             f.write(f'{taxid}\n')

diff --git a/tools/get_sbml_model/get_sbml_model.xml b/tools/get_sbml_model/get_sbml_model.xml
@@ -5,19 +5,28 @@
         <requirement type="package" version="1.11">gzip</requirement>
         <requirement type="package" version="5.19.2">python-libsbml</requirement>
         <requirement type="package" version="2.29">requests</requirement>
+        <requirement type="package" version="0.1.0">taxonid</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str($cond_src.from_src) == 'from_bigg'
             curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
-        #else
-            cp '${cond_src.input_file}' '$model' &&
         #end if
         python '$__tool_directory__/'get_infos.py
-        '$model'
-        --hostid '${cond_src.hostid}'
-        --comp '$compartments'
-        --biomass '$biomass'
-        --taxid '$taxid'
+            #if str($cond_src.from_src) == 'from_bigg'
+                '$model'
+            #else
+                '${cond_src.input_file}'
+            #end if
+            --hostid '${cond_src.hostid}'
+            --comp '$compartments'
+            --biomass '$biomass'
+        #if str($cond_src.from_src) == 'from_bigg'
+            --taxid '$taxid'
+        #else
+            python -m taxonid '${cond_src.hostid}' --output-file tmpfile
+            echo "#ID" > '$taxid'
+            cat tmpfile >> '$taxid'
+        #end if
     ]]></command>
     <inputs>
         <conditional name="cond_src">
@@ -26,8 +35,8 @@
                 <option value="from_history">Select file from the History</option>
             </param>
             <when value="from_history">
-                <param name="hostid" type="text" help="ID of the model">
-                    <validator type="empty_field" message="An ID is required"/>
+                <param name="hostid" type="text" help="Fullname of the model">
+                    <validator type="empty_field" message="The fullname of the organism is required"/>
                 </param>
                 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
             </when>
@@ -85,7 +94,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="model" format="sbml" label="${cond_src.hostid}" />
+        <when value="from_bigg">
+            <data name="model" format="sbml" label="${cond_src.hostid}" />
+        </when>
         <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />
         <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />
         <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
@@ -104,13 +115,12 @@
         <test>
             <conditional name="cond_src">
                 <param name="from_src" value="from_history" />
-                <param name="hostid" value="e_coli_core" />
+                <param name="hostid" value="Escherichia coli str. K-12 substr. MG1655" />
                 <param name="input_file" value="e_coli_core.xml" />
             </conditional>
-            <output name="model" md5="4574760460afe9e1b3388dc15f354706" />
             <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
-            <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
-            <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
+            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
+            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
             </test>
     </tests>
     <help><![CDATA[