adding job submit ENVIRONMENT and minor improvement to runWorkflow

qiita_db/processing_job.py

@@ -880,12 +880,30 @@ def submit(self, parent_job_id=None, dependent_jobs_list=None):
         # portal server that submitted the job
         url = "%s%s" % (qiita_config.base_url, qiita_config.portal_dir)
 
+        # if the word ENVIRONMENT is in the plugin_env_script we have a special
+        # case where we are going to execute some command and then wait for the
+        # plugin to return their own id (first implemented for
+        # fast-bowtie2+woltka)
+        if 'ENVIRONMENT' in plugin_env_script:
+            # the job has to be in running state so the plugin can change its`
+            # status
+            with qdb.sql_connection.TRN:
+                self._set_status('running')
+                qdb.sql_connection.TRN.commit()
+
+            create_nested_path(job_dir)
+            cmd = (f'{plugin_env_script}; {plugin_start_script} '
+                   f'{url} {self.id} {job_dir}')
+            stdout, stderr, return_value = _system_call(cmd)
+            if return_value != 0 or stderr != '':
+                self._set_error(stderr)
+            job_id = stdout
         # note that dependent jobs, such as m validator jobs marshalled into
         # n 'queues' require the job_id returned by an external scheduler such
         # as Torque's MOAB, rather than a job name that can be defined within
         # Qiita. Hence, this method must be able to handle the case where a job
         # requires metadata from a late-defined and time-sensitive source.
-        if qiita_config.plugin_launcher in ProcessingJob._launch_map:
+        elif qiita_config.plugin_launcher in ProcessingJob._launch_map:
             launcher = ProcessingJob._launch_map[qiita_config.plugin_launcher]
             if launcher['execute_in_process']:
                 # run this launcher function within this process.

qiita_db/test/test_processing_job.py

@@ -265,6 +265,24 @@ def test_submit_error(self):
                 qdb.exceptions.QiitaDBOperationNotPermittedError):
             job.submit()
 
+    def test_submit_environment(self):
+        job = _create_job()
+        software = job.command.software
+        current = software.environment_script
+
+        # temporal update and then rollback to not commit change
+        with qdb.sql_connection.TRN:
+            sql = """UPDATE qiita.software SET environment_script = %s
+                     WHERE software_id = %s"""
+            qdb.sql_connection.TRN.add(sql, [
+                f'{current} ENVIRONMENT', software.id])
+
+            job.submit()
+
+            self.assertEqual(job.status, 'error')
+
+            qdb.sql_connection.TRN.rollback()
+
     def test_complete_multiple_outputs(self):
         # This test performs the test of multiple functions at the same
         # time. "release", "release_validators" and

qiita_pet/static/js/networkVue.js

@@ -70,7 +70,7 @@ Vue.component('processing-graph', {
                     '<div class="col-md-2">' +
                       '<h4><span class="blinking-message">Start workflow:</h4></span>' +
                     '</div>' +
-                    '<div class="col-md-1">' +
+                    '<div class="col-md-2">' +
                       '<a class="btn btn-success form-control" id="run-btn"><span class="glyphicon glyphicon-play"></span> Run</a>' +
                     '</div>' +
                   '</div>' +
@@ -341,6 +341,8 @@ Vue.component('processing-graph', {
      *
      */
     runWorkflow: function() {
+      $('#run-btn').attr('disabled', true);
+      $('#run-btn').html('<span class="glyphicon glyphicon-stop"></span> Submitting');
       let vm = this;
       $.post(vm.portal + "/study/process/workflow/run/", {workflow_id: vm.workflowId}, function(data){
         bootstrapAlert("Workflow " + vm.workflowId + " submitted", "success");
@@ -351,9 +353,11 @@ Vue.component('processing-graph', {
         .fail(function(object, status, error_msg) {
           bootstrapAlert("Error submitting workflow: " + object.statusText, "danger");
         });
-      // return button to regular state
-      $('#run-btn').attr('disabled', false);
-      $('#run-btn').html('<span class="glyphicon glyphicon-play"></span> Run');
+        .always(function() {
+          // return button to regular state
+          $('#run-btn').attr('disabled', false);
+          $('#run-btn').html('<span class="glyphicon glyphicon-play"></span> Run');
+        });
     },
 
     /**