Merge pull request #17440 from mvdbeek/fix_it_templating

[23.2] Build param dict before creating entrypoint

lib/galaxy/jobs/__init__.py

@@ -1249,15 +1249,13 @@ def get_special():
 
         tool_evaluator = self._get_tool_evaluator(job)
         compute_environment = compute_environment or self.default_compute_environment(job)
-        if hasattr(self.app, "interactivetool_manager"):
-            self.interactivetools = tool_evaluator.populate_interactivetools()
-            self.app.interactivetool_manager.create_interactivetool(job, self.tool, self.interactivetools)
         tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
         (
             self.command_line,
             self.version_command_line,
             self.extra_filenames,
             self.environment_variables,
+            self.interactivetools,
         ) = tool_evaluator.build()
         job.command_line = self.command_line
 
@@ -2623,6 +2621,7 @@ def prepare(self, compute_environment=None):
                 self.version_command_line,
                 extra_filenames,
                 self.environment_variables,
+                *_,
             ) = tool_evaluator.build()
             self.extra_filenames.extend(extra_filenames)
 

lib/galaxy/tools/evaluation.py

@@ -121,6 +121,7 @@ def __init__(self, app: MinimalToolApp, tool, job, local_working_directory):
         self.environment_variables: List[Dict[str, str]] = []
         self.version_command_line: Optional[str] = None
         self.command_line: Optional[str] = None
+        self.interactivetools: List[Dict[str, Any]] = []
 
     def set_compute_environment(self, compute_environment: ComputeEnvironment, get_special: Optional[Callable] = None):
         """
@@ -514,7 +515,12 @@ def rewrite_unstructured_paths(input_values, input):
             # the paths rewritten.
             self.__walk_inputs(self.tool.inputs, param_dict, rewrite_unstructured_paths)
 
-    def populate_interactivetools(self):
+    def _create_interactivetools_entry_points(self):
+        if hasattr(self.app, "interactivetool_manager"):
+            self.interactivetools = self._populate_interactivetools_template()
+            self.app.interactivetool_manager.create_interactivetool(self.job, self.tool, self.interactivetools)
+
+    def _populate_interactivetools_template(self):
         """
         Populate InteractiveTools templated values.
         """
@@ -571,12 +577,21 @@ def build(self):
         compute environment.
         """
         config_file = self.tool.config_file
+        global_tool_logs(
+            self._create_interactivetools_entry_points, config_file, "Building Interactive Tool Entry Points"
+        )
         global_tool_logs(self._build_config_files, config_file, "Building Config Files")
         global_tool_logs(self._build_param_file, config_file, "Building Param File")
         global_tool_logs(self._build_command_line, config_file, "Building Command Line")
         global_tool_logs(self._build_version_command, config_file, "Building Version Command Line")
         global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables")
-        return self.command_line, self.version_command_line, self.extra_filenames, self.environment_variables
+        return (
+            self.command_line,
+            self.version_command_line,
+            self.extra_filenames,
+            self.environment_variables,
+            self.interactivetools,
+        )
 
     def _build_command_line(self):
         """
@@ -823,7 +838,13 @@ class PartialToolEvaluator(ToolEvaluator):
     def build(self):
         config_file = self.tool.config_file
         global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables")
-        return self.command_line, self.version_command_line, self.extra_filenames, self.environment_variables
+        return (
+            self.command_line,
+            self.version_command_line,
+            self.extra_filenames,
+            self.environment_variables,
+            self.interactivetools,
+        )
 
 
 class RemoteToolEvaluator(ToolEvaluator):
@@ -841,4 +862,10 @@ def build(self):
         global_tool_logs(self._build_param_file, config_file, "Building Param File")
         global_tool_logs(self._build_command_line, config_file, "Building Command Line")
         global_tool_logs(self._build_version_command, config_file, "Building Version Command Line")
-        return self.command_line, self.version_command_line, self.extra_filenames, self.environment_variables
+        return (
+            self.command_line,
+            self.version_command_line,
+            self.extra_filenames,
+            self.environment_variables,
+            self.interactivetools,
+        )

lib/galaxy/tools/remote_tool_eval.py

@@ -114,7 +114,7 @@ def main(TMPDIR, WORKING_DIRECTORY, IMPORT_STORE_DIRECTORY):
     )
     tool_evaluator.set_compute_environment(compute_environment=SharedComputeEnvironment(job_io=job_io, job=job_io.job))
     with open(os.path.join(WORKING_DIRECTORY, "tool_script.sh"), "a") as out:
-        command_line, version_command_line, extra_filenames, environment_variables = tool_evaluator.build()
+        command_line, version_command_line, extra_filenames, environment_variables, *_ = tool_evaluator.build()
         out.write(f'{version_command_line or ""}{command_line}')
 
 

test/functional/tools/interactivetool_simple.xml

@@ -3,7 +3,7 @@
         <container type="docker">galaxy/test-http-example:0.1</container>
     </requirements>
     <entry_points>
-        <entry_point name="Simple" requires_domain="True">
+        <entry_point name="Simple IT for $__user_email__" requires_domain="True">
             <port>7000</port>
             <url>/</url>
         </entry_point>

test/unit/app/jobs/test_job_wrapper.py

@@ -113,14 +113,11 @@ def __init__(self, app, tool, job, local_working_directory):
         self.local_working_directory = local_working_directory
         self.param_dict = {}
 
-    def populate_interactivetools(self):
-        return []
-
     def set_compute_environment(self, *args, **kwds):
         pass
 
     def build(self):
-        return TEST_COMMAND, "", [], []
+        return TEST_COMMAND, "", [], [], []
 
 
 class MockJobQueue:

test/unit/app/tools/test_evaluation.py

@@ -139,7 +139,7 @@ def test_configfiles_evaluation(self):
         self.tool.config_files.append(("conf1", None, "$thresh"))
         self.tool._command_line = "prog1 $conf1"
         self._set_compute_environment()
-        command_line, _, extra_filenames, _ = self.evaluator.build()
+        command_line, _, extra_filenames, *_ = self.evaluator.build()
         assert len(extra_filenames) == 1
         config_filename = extra_filenames[0]
         config_basename = os.path.basename(config_filename)