fixing issues from 2021.07

qiita_db/metadata_template/prep_template.py

@@ -884,25 +884,24 @@ def _get_predecessors(workflow, node):
                     job_params = qdb.software.Parameters.load(
                         cmd, values_dict=params)
 
-                    if job_params in previous_jobs.values():
+                    if params in previous_jobs.values():
                         for x, y in previous_jobs.items():
-                            if job_params == y:
+                            if params == y:
                                 current_job = x
-                        continue
-
-                    if workflow is None:
-                        PW = qdb.processing_job.ProcessingWorkflow
-                        workflow = PW.from_scratch(user, job_params)
-                        current_job = [j for j in workflow.graph.nodes()][0]
                     else:
-                        if previous_job is None:
-                            current_job = workflow.add(
-                                job_params, req_params=req_params)
+                        if workflow is None:
+                            PW = qdb.processing_job.ProcessingWorkflow
+                            workflow = PW.from_scratch(user, job_params)
+                            current_job = [
+                                j for j in workflow.graph.nodes()][0]
                         else:
-                            current_job = workflow.add(
-                                job_params, req_params=req_params,
-                                connections={previous_job: connections})
-
-                    previous_jobs[current_job] = job_params
+                            if previous_job is None:
+                                current_job = workflow.add(
+                                    job_params, req_params=req_params)
+                            else:
+                                current_job = workflow.add(
+                                    job_params, req_params=req_params,
+                                    connections={previous_job: connections})
+                        previous_jobs[current_job] = params
 
         return workflow

qiita_db/metadata_template/test/test_prep_template.py

@@ -1346,13 +1346,64 @@ def test_artifact_setter(self):
             self.filepaths, "FASTQ", prep_template=pt)
         self.assertEqual(pt.artifact, artifact)
 
-        # here we can test that we can properly create a workflow
+        # here we can test that we can properly create a workflow but we are
+        # going to add lot more steps to make it more complex by adding a
+        # couple of new scenarios
+        # 1/2. adds a new path that should be kept separate all the way; this
+        #      is to emulate what happens with different trimming (different
+        #      default parameter) and deblur (same for each of the previous
+        #      steps)
+        sql = """
+            INSERT INTO qiita.default_workflow_node (
+                default_workflow_id, default_parameter_set_id)
+            VALUES (1, 2), (1, 10);
+            INSERT INTO qiita.default_workflow_edge (
+                parent_id, child_id)
+            VALUES (7, 8);
+            INSERT INTO qiita.default_workflow_edge_connections (
+                default_workflow_edge_id, parent_output_id, child_input_id)
+            VALUES (4, 1, 3)"""
+        qdb.sql_connection.perform_as_transaction(sql)
+        # 2/2. adds a new path that should be kept together and then separate;
+        #      this is to simulate what happens with MTX/WGS processing, one
+        #      single QC step (together) and 2 separete profilers
+        sql = """
+            INSERT INTO qiita.default_parameter_set (
+                command_id, parameter_set_name, parameter_set)
+            VALUES (3, '100%',
+                    ('{"reference":1,"sortmerna_e_value":1,'
+                     || '"sortmerna_max_pos":'
+                     || '10000,"similarity":1.0,"sortmerna_coverage":1.00,'
+                     || '"threads":1}')::json);
+            INSERT INTO qiita.default_workflow_node (
+                default_workflow_id, default_parameter_set_id)
+            VALUES (1, 17);
+            INSERT INTO qiita.default_workflow_edge (
+                parent_id, child_id)
+            VALUES (7, 9);
+            INSERT INTO qiita.default_workflow_edge_connections (
+                default_workflow_edge_id, parent_output_id, child_input_id)
+            VALUES (5, 1, 3)
+            """
+        qdb.sql_connection.perform_as_transaction(sql)
+        # Finally, we need to "activate" the merging scheme values of the
+        # commands so they are actually different:
+        # 31->'Pick closed-reference OTUs', 6->'Split libraries FASTQ'
+        sql = """
+            UPDATE qiita.command_parameter
+            SET check_biom_merge = true
+            WHERE command_parameter_id IN (31, 6)"""
+        qdb.sql_connection.perform_as_transaction(sql)
+
         wk = pt.add_default_workflow(qdb.user.User('test@foo.bar'))
-        self.assertEqual(len(wk.graph.nodes), 2)
-        self.assertEqual(len(wk.graph.edges), 1)
-        self.assertEqual(
+        self.assertEqual(len(wk.graph.nodes), 5)
+        self.assertEqual(len(wk.graph.edges), 3)
+        self.assertCountEqual(
             [x.command.name for x in wk.graph.nodes],
-            ['Split libraries FASTQ', 'Pick closed-reference OTUs'])
+            # we should have 2 split libraries and 3 close reference
+            ['Split libraries FASTQ', 'Split libraries FASTQ',
+             'Pick closed-reference OTUs', 'Pick closed-reference OTUs',
+             'Pick closed-reference OTUs'])
 
         # now let's try to generate again and it should fail cause the jobs
         # are alrady created

qiita_pet/handlers/study_handlers/processing.py

@@ -30,6 +30,9 @@ class ListOptionsHandler(BaseHandler):
     def get(self):
         command_id = self.get_argument("command_id")
         artifact_id = self.get_argument("artifact_id")
+        # if the artifact id has ':' it means that it's a job in construction
+        if ':' in artifact_id:
+            artifact_id = None
         self.write(list_options_handler_get_req(command_id, artifact_id))
 
 

qiita_pet/handlers/study_handlers/tests/test_processing.py

@@ -15,13 +15,54 @@
 
 
 class TestListCommandsHandler(TestHandlerBase):
-    # TODO: Missing tests
-    pass
+    def test_get(self):
+        response = self.get('/study/process/commands/',
+                            {'artifact_id': '8', 'include_analysis': 'true'})
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success', 'message': '', 'commands': [
+            {'id': 9, 'command': 'Summarize Taxa',
+             'output': [['taxa_summary', 'taxa_summary']]},
+            {'id': 10, 'command': 'Beta Diversity', 'output': [
+                ['distance_matrix', 'beta_div_plots']]},
+            {'id': 11, 'command': 'Alpha Rarefaction', 'output': [
+                ['rarefaction_curves', 'rarefaction_curves']]},
+            {'id': 12, 'command': 'Single Rarefaction', 'output': [
+                ['rarefied_table', 'BIOM']]}]}
+
+        response = self.get('/study/process/commands/',
+                            {'artifact_id': '3', 'include_analysis': 'false'})
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success', 'message': '', 'commands': [
+            {'id': 3, 'command': 'Pick closed-reference OTUs', 'output': [
+                ['OTU table', 'BIOM']]}]}
+        self.assertEqual(loads(response.body), exp)
 
 
 class TestListOptionsHandler(TestHandlerBase):
-    # TODO: Missing tests
-    pass
+    def test_get(self):
+        response = self.get('/study/process/commands/options/',
+                            {'command_id': '3', 'artifact_id': '8'})
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success', 'message': '', 'options': [
+            {'id': 10, 'name': 'Defaults', 'values':
+             {'reference': 1, 'sortmerna_e_value': 1,
+              'sortmerna_max_pos': 10000, 'similarity': 0.97,
+              'sortmerna_coverage': 0.97, 'threads': 1}}],
+              'req_options': {'input_data': ['artifact', ['Demultiplexed']]},
+              'opt_options': {'reference': ['reference', '1'],
+                              'sortmerna_e_value': ['float', '1'],
+                              'sortmerna_max_pos': ['integer', '10000'],
+                              'similarity': ['float', '0.97'],
+                              'sortmerna_coverage': ['float', '0.97'],
+                              'threads': ['integer', '1']}}
+        self.assertEqual(loads(response.body), exp)
+
+        # test that it works fine with a job_id:artifact_type
+        response = self.get('/study/process/commands/options/',
+                            {'command_id': '3',
+                             'artifact_id': 'job_id:artifact_type'})
+        self.assertEqual(response.code, 200)
+        self.assertEqual(loads(response.body), exp)
 
 
 class TestJobAJAX(TestHandlerBase):

qiita_pet/static/js/networkVue.js

@@ -1145,8 +1145,8 @@ Vue.component('processing-graph', {
         '<td>' + circle_statuses.join('') + '</td>' +
         '<td rowspan="2" width="20px">&nbsp;</td>' +
         '<td rowspan="2">&nbsp;&nbsp;&nbsp;</td>' +
-        '<td rowspan="2" align="center">' +
-            '<a class="btn btn-success form-control" id="add-default-workflow"><span class="glyphicon glyphicon-flash"></span> Add Default Workflow</a>' +
+        '<td rowspan="2" align="center" id="add-default-workflow">' +
+            '<a class="btn btn-success form-control" id="add-default-workflow-btn"><span class="glyphicon glyphicon-flash"></span> Add Default Workflow</a>' +
              "<br/><br/><a href='https://qiita.ucsd.edu/workflows/' target='_blank'> "+
                 '<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-exclamation-triangle" viewBox="0 0 16 16">' +
                     '<path d="M7.938 2.016A.13.13 0 0 1 8.002 2a.13.13 0 0 1 .063.016.146.146 0 0 1 .054.057l6.857 11.667c.036.06.035.124.002.183a.163.163 0 0 1-.054.06.116.116 0 0 ' +
@@ -1164,18 +1164,18 @@ Vue.component('processing-graph', {
     '</table>';
     $('#circle-explanation').html(full_text);
 
-    $('#add-default-workflow').on('click', function () {
+    $('#add-default-workflow-btn').on('click', function () {
       $('#add-default-workflow').attr('disabled', true);
-      document.getElementById('add-default-workflow').innerHTML = 'Submitting!';
+      document.getElementById('add-default-workflow-btn').innerHTML = 'Submitting!';
       $.post(vm.portal + '/study/process/workflow/default/', {prep_id: vm.elementId}, function(data) {
         if (data['msg_error'] !== null){
-          $('#add-default-workflow').attr('disabled', false);
+          $('#add-default-workflow-btn').attr('disabled', false);
           bootstrapAlert('Error generating workflow: ' + data['msg_error'].replace("\n", "<br/>"));
         } else {
           vm.updateGraph();
         }
       });
-      document.getElementById('add-default-workflow').innerHTML = ' Add Default Workflow';
+      document.getElementById('add-default-workflow-btn').innerHTML = ' Add Default Workflow';
     });
 
     // This call to udpate graph will take care of updating the jobs

qiita_pet/templates/study_ajax/add_artifact.html

@@ -52,6 +52,7 @@
     // Modify the submit action of the form to use AJAX
     $("#create-artifact-form").submit(function(event){
       event.preventDefault();
+      $('#add-files-btn').prop('disabled', true);
       // Add the prep template as a parameter
       $('<input>').attr({
         type: 'hidden',
@@ -82,6 +83,7 @@
           bootstrapAlert("Error: " + error_msg + "  " + status, "danger");
         }
       });
+      $('#add-files-btn').prop('disabled', false);
     });
   });
 </script>
@@ -111,7 +113,7 @@ <h4><i>No files attached to this preparation</i></h4>
   </div>
   <div class="row" id="submit-div" data-error-count="0" hidden>
     <div class="col-md-12" style="margin-top: 5px;">
-      <input type="submit" class="btn btn-sm btn-success" onclick="this.disabled=true;" value="Add files">
+      <input type="submit" class="btn btn-sm btn-success" id="add-files-btn" value="Add files">
     </div>
   </div>
 </form>