Merge pull request #3129 from mvdbeek/conda_error_reporting

Pass dependency shell command errors to log

lib/galaxy/tools/deps/commands.py

@@ -34,13 +34,19 @@ def shell(cmds, env=None, **kwds):
     """Run shell commands with `shell_process` and wait."""
     sys = kwds.get("sys", _sys)
     assert sys is not None
-    p = shell_process(cmds, env, **kwds)
     if redirecting_io(sys=sys):
+        p = shell_process(cmds, env, **kwds)
         redirect_aware_commmunicate(p, sys=sys)
         exit = p.returncode
         return exit
     else:
-        return p.wait()
+        kwds['stdout'] = subprocess.PIPE
+        kwds['stderr'] = subprocess.PIPE
+        p = shell_process(cmds, env, **kwds)
+        stdout, stderr = p.communicate()
+        if p.returncode != 0:
+            raise CommandLineException(cmds, stdout, stderr, p.returncode)
+        return p.returncode
 
 
 def shell_process(cmds, env=None, **kwds):
@@ -122,11 +128,12 @@ def download_command(url, to=STDOUT_INDICATOR, quote_url=False):
 class CommandLineException(Exception):
     """An exception indicating a non-zero command-line exit."""
 
-    def __init__(self, command, stdout, stderr):
+    def __init__(self, command, stdout, stderr, returncode):
         """Construct a CommandLineException from command and standard I/O."""
         self.command = command
         self.stdout = stdout
         self.stderr = stderr
+        self.returncode = returncode
         self.message = ("Failed to execute command-line %s, stderr was:\n"
                         "-------->>begin stderr<<--------\n"
                         "%s\n"

lib/galaxy/tools/deps/conda_util.py

@@ -183,7 +183,12 @@ class CondaContext(installable.InstallableContext):
         condarc_override = self.condarc_override
         if condarc_override:
             env["CONDARC"] = condarc_override
-        return self.shell_exec(command, env=env)
+        log.debug("Executing command: %s", command)
+        try:
+            return self.shell_exec(command, env=env)
+        except commands.CommandLineException as e:
+            log.warning(e)
+            return e.returncode
 
     def exec_create(self, args):
         create_base_args = [

lib/galaxy/tools/deps/resolvers/conda.py

@@ -136,7 +136,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         if not is_installed:
             return NullDependency(version=version, name=name)
 
-        # Have installed conda_target and job_directory to send it too.
+        # Have installed conda_target and job_directory to send it to.
         # If dependency is for metadata generation, store environment in conda-metadata-env
         if kwds.get("metadata", False):
             conda_env = "conda-metadata-env"
@@ -149,7 +149,6 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
             copy=self.copy_dependencies,
             conda_context=self.conda_context,
         )
-
         if not exit_code:
             return CondaDependency(
                 self.conda_context.activate,
@@ -159,12 +158,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
                 version
             )
         else:
-            if len(conda_environment) > 79:
-                # TODO: remove this once conda_build version 2 is released and packages have been rebuilt.
-                raise Exception("Conda dependency failed to build job environment. "
-                                "This is most likely a limitation in conda. "
-                                "You can try to shorten the path to the job_working_directory.")
-            raise Exception("Conda dependency seemingly installed but failed to build job environment.")
+            return NullDependency(version=version, name=name)
 
     def list_dependencies(self):
         for install_target in installed_conda_targets(self.conda_context):