SWISS-MODEL API tool - Use credentials instead of parameter for tokens

Author: RZ9082

tools/swissmodel_modelling_api/sm_api_wrapper.py

@@ -286,13 +286,7 @@ def _parse_args():
     metas = {
         "outdir": "<OUTPUT DIRECTORY>",
         "target_sequences": "<SEQUENCE[S]>",
-        "token": "<TOKEN>",
     }
-    parser.add_argument(
-        "token",
-        help="Authentication token for SWISS-MODEL",
-        metavar=metas["token"],
-    )
     parser.add_argument(
         "outdir",
         help="Directory to store results in",
@@ -377,20 +371,27 @@ def _main():
     """Run as script."""
     opts = _parse_args()
 
+    token = os.getenv("SWISSMODEL_API_TOKEN")
+    if not token:
+        print(
+            "SWISS-MODEL token is not provided in credentials!",
+            file=sys.stderr,
+        )
+        sys.exit(1)
     target_sequences = _defastarise_targets(opts.target_sequences)
     # determine class
     whsprr = None
     if opts.project_type.lower() == "automodel":
         whsprr = _AutoModelWhisperer(
-            target_sequences, opts.token, project_title=opts.project_title
+            target_sequences, token, project_title=opts.project_title
         )
     elif opts.project_type.lower() == "alignment":
         template_sequence = _defastarise_targets([opts.template_sequence])
         assert len(template_sequence) == 1
         template_sequence = template_sequence[0]
         whsprr = _AlignmentWhisperer(
             target_sequences,
-            opts.token,
+            token,
             template_sequence,
             opts.template_seqres_offset,
             opts.pdb_id,
@@ -401,7 +402,7 @@ def _main():
     elif opts.project_type.lower() == "usertemplate":
         whsprr = _UserTemplateWhisperer(
             target_sequences,
-            opts.token,
+            token,
             opts.template_file,
             project_title=opts.project_title,
         )

tools/swissmodel_modelling_api/swissmodel_api.xml

@@ -1,13 +1,20 @@
-<tool name="SWISS-MODEL Modelling API" id="swissmodel_modelling_api" profile="21.05" version="2.0.0">
+<tool name="SWISS-MODEL Modelling API" id="swissmodel_modelling_api" profile="25.1" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>
         Fully automated protein structure homology-modelling
     </description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <xrefs>
         <xref type="bio.tools">swiss_model</xref>
     </xrefs>
     <requirements>
         <requirement type="package" version="3.11">python</requirement>
         <requirement type="package" version="2.32.5">requests</requirement>
+        <credentials name="swissmodel_api_credentials" version="1.0" label="SWISS-MODEL API Credentials" description="Credentials for accessing SWISS-MODEL API">
+            <secret name="swissmodel_api_token" inject_as_env="SWISSMODEL_API_TOKEN" optional="false" label="SWISS-MODEL API token" description="Token to authenticate to the SWISS-MODEL API. Can be managed on your https://swissmodel.expasy.org/login_page"/>
+        </credentials>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 mkdir -p 'output_dir/'
@@ -27,7 +34,7 @@ mkdir -p 'output_dir/'
                             --template-file '${template_file}'
                           #end if
                           '${project.project_type}'
-                          '${token}' output_dir
+                          output_dir
                           #if $project_type == 'alignment'
                             '${target_sequence}'
                           #else
@@ -39,12 +46,6 @@ mkdir -p 'output_dir/'
 ]]>
     </command>
     <inputs>
-        <param name="token" type="text" optional="false" label="API token">
-            <help><![CDATA[
-Token to authenticate to the SWISS-MODEL API. Can be managed on your
-<a href="https://swissmodel.expasy.org/login_page" target="_blank"> SWISS-MODEL account</a> page.
-            ]]></help>
-        </param>
         <param name="project_title" type="text" value="Untitled project" optional="true" label="Project title"/>
         <conditional name="project">
             <param name="project_type" type="select" value="automodel" optional="false" label="Modelling setup" display="radio">
@@ -140,7 +141,7 @@ sequence.
             </assert_stderr>
         </test>
         <!-- with sequences, everything else empty, fail -->
-        <test expect_exit_code="2" expect_failure="true">
+        <test expect_exit_code="1" expect_failure="true">
             <conditional name="project">
                 <repeat name="target_list">
                     <param name="sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGL"/>
@@ -150,7 +151,7 @@ sequence.
                 </repeat>
             </conditional>
             <assert_stderr>
-                <has_line line="Argument of '&lt;TOKEN&gt;' can not be an empty string"/>
+                <has_line line="SWISS-MODEL token is not provided in credentials!"/>
             </assert_stderr>
         </test>
         <!-- sequence and token (complete automodel job), fail (no real token) -->
@@ -216,7 +217,7 @@ sequence.
             </assert_stderr>
         </test>
         <!-- alignment mode tests, with sequence, fail -->
-        <test expect_exit_code="2" expect_failure="true">
+        <test expect_exit_code="1" expect_failure="true">
             <conditional name="project">
                 <param name="assembly_id" value="0"/>
                 <param name="auth_asym_id" value="A"/>
@@ -227,7 +228,7 @@ sequence.
                 <param name="template_sequence" value="MVVKAVCVINGDAKGTVFFEQESSGTPV"/>
             </conditional>
             <assert_stderr>
-                <has_line line="Argument of '&lt;TOKEN&gt;' can not be an empty string"/>
+                <has_line line="SWISS-MODEL token is not provided in credentials!"/>
             </assert_stderr>
         </test>
         <!-- alignment mode tests, with token, fail -->
@@ -257,7 +258,7 @@ sequence.
             </assert_stderr>
         </test>
         <!-- usertemplate mode tests, with sequence, fail -->
-        <test expect_exit_code="2" expect_failure="true">
+        <test expect_exit_code="1" expect_failure="true">
             <conditional name="project">
                 <param name="project_type" value="usertemplate"/>
                 <param name="template_file" value="model_01.pdb"/>
@@ -269,7 +270,7 @@ sequence.
                 </repeat>
             </conditional>
             <assert_stderr>
-                <has_line line="Argument of '&lt;TOKEN&gt;' can not be an empty string"/>
+                <has_line line="SWISS-MODEL token is not provided in credentials!"/>
             </assert_stderr>
         </test>
         <!-- usertemplate mode tests, with token, fail -->