Merge pull request #2200 from antgonza/partial-2188

partial fix -- 2188

Author: ElDeveloper

qiita_pet/handlers/api_proxy/__init__.py

@@ -34,10 +34,9 @@
                        artifact_patch_request, artifact_get_info)
 from .ontology import ontology_patch_handler
 from .processing import (
-    list_commands_handler_get_req, process_artifact_handler_get_req,
-    list_options_handler_get_req, workflow_handler_post_req,
-    workflow_handler_patch_req, workflow_run_post_req,
-    job_ajax_get_req)
+    list_commands_handler_get_req, list_options_handler_get_req,
+    workflow_handler_post_req, workflow_handler_patch_req,
+    workflow_run_post_req, job_ajax_get_req)
 from .user import (user_jobs_get_req)
 
 __version__ = "0.2.0-dev"

qiita_pet/handlers/api_proxy/processing.py

@@ -10,37 +10,10 @@
 
 from qiita_db.user import User
 from qiita_db.software import Command, Parameters, DefaultParameters
-from qiita_db.artifact import Artifact
 from qiita_db.processing_job import ProcessingWorkflow, ProcessingJob
 from qiita_db.exceptions import QiitaDBUnknownIDError
 
 
-def process_artifact_handler_get_req(artifact_id):
-    """Returns the information for the process artifact handler
-
-    Parameters
-    ----------
-    artifact_id : int
-        The artifact to be processed
-
-    Returns
-    -------
-    dict of str
-        A dictionary containing the artifact information
-        {'status': str,
-         'message': str,
-         'name': str,
-         'type': str}
-    """
-    artifact = Artifact(artifact_id)
-
-    return {'status': 'success',
-            'message': '',
-            'name': artifact.name,
-            'type': artifact.artifact_type,
-            'study_id': artifact.study.id}
-
-
 def list_commands_handler_get_req(artifact_types, exclude_analysis):
     """Retrieves the commands that can process the given artifact types
 

qiita_pet/handlers/api_proxy/tests/test_processing.py

@@ -13,29 +13,11 @@
 from qiita_db.software import Command, Parameters
 from qiita_db.user import User
 from qiita_pet.handlers.api_proxy.processing import (
-    process_artifact_handler_get_req, list_commands_handler_get_req,
-    list_options_handler_get_req, workflow_handler_post_req,
-    workflow_handler_patch_req, job_ajax_get_req)
+    list_commands_handler_get_req, list_options_handler_get_req,
+    workflow_handler_post_req, workflow_handler_patch_req, job_ajax_get_req)
 
 
 class TestProcessingAPIReadOnly(TestCase):
-    def test_process_artifact_handler_get_req(self):
-        obs = process_artifact_handler_get_req(1)
-        exp = {'status': 'success',
-               'message': '',
-               'name': 'Raw data 1',
-               'type': 'FASTQ',
-               'study_id': 1}
-        self.assertEqual(obs, exp)
-
-        obs = process_artifact_handler_get_req(2)
-        exp = {'status': 'success',
-               'message': '',
-               'name': 'Demultiplexed 1',
-               'type': 'Demultiplexed',
-               'study_id': 1}
-        self.assertEqual(obs, exp)
-
     def test_list_commands_handler_get_req(self):
         obs = list_commands_handler_get_req('FASTQ', True)
         exp = {'status': 'success',

qiita_pet/handlers/study_handlers/__init__.py

@@ -17,9 +17,8 @@
 from .prep_template import (
     PrepTemplateGraphAJAX, PrepTemplateAJAX, PrepFilesHandler,
     NewPrepTemplateAjax, PrepTemplateSummaryAJAX)
-from .processing import (ProcessArtifactHandler, ListCommandsHandler,
-                         ListOptionsHandler, WorkflowHandler,
-                         WorkflowRunHandler, JobAJAX)
+from .processing import (ListCommandsHandler, ListOptionsHandler,
+                         WorkflowHandler, WorkflowRunHandler, JobAJAX)
 from .artifact import (ArtifactGraphAJAX, NewArtifactHandler,
                        ArtifactAdminAJAX, ArtifactGetSamples, ArtifactGetInfo)
 from .sample_template import SampleTemplateAJAX, SampleAJAX
@@ -29,7 +28,7 @@
            'VAMPSHandler', 'SearchStudiesAJAX', 'PrepTemplateGraphAJAX',
            'ArtifactGraphAJAX', 'ArtifactAdminAJAX', 'StudyIndexHandler',
            'StudyBaseInfoAJAX', 'SampleTemplateAJAX', 'PrepTemplateAJAX',
-           'NewArtifactHandler', 'PrepFilesHandler', 'ProcessArtifactHandler',
+           'NewArtifactHandler', 'PrepFilesHandler',
            'ListCommandsHandler', 'ListOptionsHandler', 'SampleAJAX',
            'StudyDeleteAjax', 'NewPrepTemplateAjax',
            'DataTypesMenuAJAX', 'StudyFilesAJAX', 'PrepTemplateSummaryAJAX',

qiita_pet/handlers/study_handlers/processing.py

@@ -10,24 +10,13 @@
 
 from tornado.web import authenticated
 
-from qiita_pet.handlers.util import to_int
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.api_proxy import (
-    list_commands_handler_get_req, process_artifact_handler_get_req,
-    list_options_handler_get_req, workflow_handler_post_req,
-    workflow_handler_patch_req, job_ajax_get_req,
+    list_commands_handler_get_req, list_options_handler_get_req,
+    workflow_handler_post_req, workflow_handler_patch_req, job_ajax_get_req,
     workflow_run_post_req)
 
 
-class ProcessArtifactHandler(BaseHandler):
-    @authenticated
-    def get(self):
-        artifact_id = to_int(self.get_argument('artifact_id'))
-        res = process_artifact_handler_get_req(artifact_id)
-        res['artifact_id'] = artifact_id
-        self.render('study_ajax/processing_artifact.html', **res)
-
-
 class ListCommandsHandler(BaseHandler):
     @authenticated
     def get(self):

qiita_pet/handlers/study_handlers/tests/test_processing.py

@@ -10,11 +10,6 @@
 from qiita_pet.test.tornado_test_base import TestHandlerBase
 
 
-class ProcessArtifactHandler(TestHandlerBase):
-    # TODO: Missing tests
-    pass
-
-
 class ListCommandsHandler(TestHandlerBase):
     # TODO: Missing tests
     pass

qiita_pet/templates/artifact_ajax/processing_artifact.html

@@ -400,7 +400,9 @@
         var sel = $('<select>').appendTo($colDiv).attr('id', 'command-sel').attr('name', 'command').addClass('form-control').attr('placeholder', 'Choose command...');
         sel.append($("<option>").attr('value', "").text("Choose command...").prop('disabled', true).prop('selected', true));
         for(var i=0; i<data.commands.length; i++) {
-          sel.append($("<option>").attr('value', data.commands[i].id).text(data.commands[i].command));
+          if (data.commands[i].output.length != 0) {
+            sel.append($("<option>").attr('value', data.commands[i].id).text(data.commands[i].command));
+          }
         }
         sel.change(function(event) {
           $("#cmd-opts-div").empty();