Merge pull request #3201 from antgonza/fix-3087

fix #3087

Author: charles-cowart

qiita_pet/handlers/api_proxy/processing.py

@@ -7,6 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from json import loads, dumps
+from collections import defaultdict
 
 from qiita_db.user import User
 from qiita_db.artifact import Artifact
@@ -80,18 +81,30 @@ def list_options_handler_get_req(command_id, artifact_id=None):
         A dictionary containing the commands information
         {'status': str,
          'message': str,
-         'options': list of dicts of {'id: str', 'name': str,
-                                      'values': dict of {str: str}}}
+         'options': list of dicts of {'id: str',
+                                      'name': str,
+                                      'values': dict of {str: str}},
+         'req_options': dict,
+         'opt_options': dict,
+         'extra_artifacts': dict}
     """
     def _helper_process_params(params):
         return dumps(
             {k: str(v).lower() for k, v in params.items()}, sort_keys=True)
 
     command = Command(command_id)
-    rparamers = command.required_parameters.keys()
+    rparamers = []
+    extra_atypes = []
+    analysis = None
+    for name, (type, atype) in command.required_parameters.items():
+        rparamers.append(name)
+        # [0] cause there is only one element
+        extra_atypes.append(atype[0])
+
     eparams = []
     if artifact_id is not None:
         artifact = Artifact(artifact_id)
+        analysis = artifact.analysis
         for job in artifact.jobs(cmd=command):
             jstatus = job.status
             outputs = job.outputs if job.status == 'success' else None
@@ -104,14 +117,27 @@ def _helper_process_params(params):
                 del params[k]
             eparams.append(_helper_process_params(params))
 
+        # removing this artifact from extra_artifacts
+        if artifact.artifact_type in extra_atypes:
+            extra_atypes.remove(artifact.artifact_type)
+
+    extra_artifacts = defaultdict(list)
+    if analysis is not None:
+        analysis_artifacts = analysis.artifacts
+        for aa in analysis_artifacts:
+            atype = aa.artifact_type
+            if artifact_id != aa.id and atype in extra_atypes:
+                extra_artifacts[atype].append((aa.id, aa.name))
+
     options = [{'id': p.id, 'name': p.name, 'values': p.values}
                for p in command.default_parameter_sets
                if _helper_process_params(p.values) not in eparams]
     return {'status': 'success',
             'message': '',
             'options': options,
             'req_options': command.required_parameters,
-            'opt_options': command.optional_parameters}
+            'opt_options': command.optional_parameters,
+            'extra_artifacts': extra_artifacts}
 
 
 def workflow_handler_post_req(user_id, command_id, params):

qiita_pet/handlers/api_proxy/tests/test_processing.py

@@ -68,14 +68,16 @@ def test_list_options_handler_get_req(self):
                                'sortmerna_coverage': ['float', '0.97'],
                                'sortmerna_e_value': ['float', '1'],
                                'sortmerna_max_pos': ['integer', '10000'],
-                               'threads': ['integer', '1']}}
+                               'threads': ['integer', '1']},
+               'extra_artifacts': {}}
         # First check that the keys are the same
         self.assertCountEqual(obs, exp)
         self.assertEqual(obs['status'], exp['status'])
         self.assertEqual(obs['message'], exp['message'])
         self.assertEqual(obs['options'], exp['options'])
         self.assertEqual(obs['req_options'], exp['req_options'])
         self.assertEqual(obs['opt_options'], exp['opt_options'])
+        self.assertEqual(obs['extra_artifacts'], exp['extra_artifacts'])
 
     def test_job_ajax_get_req(self):
         obs = job_ajax_get_req("063e553b-327c-4818-ab4a-adfe58e49860")

qiita_pet/handlers/study_handlers/tests/test_processing.py

@@ -54,7 +54,8 @@ def test_get(self):
                               'sortmerna_max_pos': ['integer', '10000'],
                               'similarity': ['float', '0.97'],
                               'sortmerna_coverage': ['float', '0.97'],
-                              'threads': ['integer', '1']}}
+                              'threads': ['integer', '1']},
+              'extra_artifacts': {}}
         self.assertEqual(loads(response.body), exp)
 
         # test that it works fine with a job_id:artifact_type

qiita_pet/static/js/networkVue.js

@@ -555,6 +555,14 @@ Vue.component('processing-graph', {
             // Put first the required parameters
             $("#cmd-opts-div").append($('<h4>').text('Required parameters:'));
             var keys = Object.keys(data.req_options).sort(function(a, b){return a.localeCompare(b, 'en', {'sensitivity': 'base'});});
+
+            // adding extra artifacts to sel_artifacts_info so they are added to the GUI
+            $.each(data.extra_artifacts, function(artifact_type, artifacts) {
+              $.each(artifacts, function(index, adata) {
+                sel_artifacts_info[adata[0]] = {'type': artifact_type, 'name': adata[1] + ' [' + adata[0] + ']'}
+              });
+            });
+
             for (var i = 0; i < keys.length; i++) {
               var key = keys[i];
               vm.loadParameterGUI(key, data.req_options[key], sel_artifacts_info, $("#cmd-opts-div"));
@@ -748,7 +756,16 @@ Vue.component('processing-graph', {
         style: {
           'curve-style': 'bezier',
           'target-arrow-shape': 'triangle'
-        }},
+        }}, {
+        selector: 'node.highlight',
+        style: {
+         'border-width': '5px'
+        }}, {
+        selector: 'edge.highlight',
+        style: {
+          'line-color': '#333',
+          'target-arrow-color': '#333'
+        }}
       ];
       var panzoom_options =	{
         zoomOnly: true,
@@ -787,9 +804,17 @@ Vue.component('processing-graph', {
       });
 
       vm.network.on('tap', 'node', function (evt) {
-        var data = evt.target.data();
+        var target = evt.target;
+        var data = target.data();
         var element_id = data.id;
 
+        // removing all highlight classes from network and highlighting the
+        // element that was just selected
+        vm.network.nodes().removeClass('highlight');
+        vm.network.edges().removeClass('highlight');
+        target.addClass('highlight');
+        target.connectedEdges().addClass('highlight');
+
         if (data.group === 'artifact') {
           vm.populateContentArtifact(element_id);
         } else if (data.group === 'deleting') {