Refactoring the refactor (I): Fix prep info creation

qiita_db/util.py

@@ -444,6 +444,7 @@ def get_files_from_uploads_folders(study_id):
     list
         List of the filepaths for upload for that study
     """
+    study_id = str(study_id)
     fp = []
     for pid, p in get_mountpoint("uploads", retrieve_all=True):
         t = join(p, study_id)

qiita_pet/handlers/api_proxy/__init__.py

@@ -20,7 +20,8 @@
     prep_template_summary_get_req, prep_template_post_req,
     prep_template_put_req, prep_template_delete_req, prep_template_get_req,
     prep_template_graph_get_req, prep_template_filepaths_get_req,
-    ena_ontology_get_req, prep_template_samples_get_req)
+    ena_ontology_get_req, prep_template_samples_get_req,
+    new_prep_template_get_req)
 from .studies import (
     data_types_get_req, study_get_req, study_prep_get_req, study_delete_req)
 from .artifact import (artifact_graph_get_req, artifact_types_get_req,
@@ -43,4 +44,4 @@
            'artifact_post_req', 'ena_ontology_get_req',
            'sample_template_meta_cats_get_req',
            'sample_template_samples_get_req', 'prep_template_samples_get_req',
-           'sample_template_category_get_req']
+           'sample_template_category_get_req', 'new_prep_template_get_req']

qiita_pet/handlers/api_proxy/prep_template.py

@@ -14,12 +14,45 @@
 from qiita_core.util import execute_as_transaction
 from qiita_pet.handlers.api_proxy.util import check_access, check_fp
 from qiita_db.metadata_template.util import load_template_to_dataframe
-from qiita_db.util import convert_to_id
+from qiita_db.util import convert_to_id, get_files_from_uploads_folders
 from qiita_db.study import Study
 from qiita_db.ontology import Ontology
 from qiita_db.metadata_template.prep_template import PrepTemplate
 
 
+def new_prep_template_get_req(study_id):
+    """
+    Parameters
+    ----------
+    study_id : int
+        The study id
+
+    Returns
+    -------
+    (list of str, list of str, dict of {str: list of str})
+        The list of txt,csv files in the upload dir for the given study
+        The list of available data types
+        The investigation type ontology information
+    """
+    prep_files = [f for _, f in get_files_from_uploads_folders(study_id)
+                  if f.endswith(('txt', 'tsv'))]
+    data_types = sorted(Study.all_data_types())
+
+    # Get all the ENA terms for the investigation type
+    ontology = Ontology(convert_to_id('ENA', 'ontology'))
+    ena_terms = sorted(ontology.terms)
+    # make "Other" last on the list
+    ena_terms.remove('Other')
+    ena_terms.append('Other')
+
+    ontology_info = {'ENA': ena_terms,
+                     'User': sorted(ontology.user_defined_terms)}
+    return {'status': 'success',
+            'prep_files': prep_files,
+            'data_types': data_types,
+            'ontology': ontology_info}
+
+
 @execute_as_transaction
 def _process_investigation_type(inv_type, user_def_type, new_type):
     """Return the investigation_type and add it to the ontology if needed
@@ -197,11 +230,10 @@ def prep_template_post_req(study_id, user_id, prep_template, data_type,
     prep = None
     try:
         with warnings.catch_warnings(record=True) as warns:
-            data_type_id = convert_to_id(data_type, 'data_type')
             # deleting previous uploads and inserting new one
-            prep = PrepTemplate.create(load_template_to_dataframe(fp_rpt),
-                                       Study(int(study_id)), int(data_type_id),
-                                       investigation_type=investigation_type)
+            prep = PrepTemplate.create(
+                load_template_to_dataframe(fp_rpt), Study(study_id), data_type,
+                investigation_type=investigation_type)
             remove(fp_rpt)
 
             # join all the warning messages into one. Note that this info

qiita_pet/handlers/api_proxy/studies.py

@@ -148,18 +148,23 @@ def study_prep_get_req(study_id, user_id):
         prep_info[dtype] = []
         for prep in study.prep_templates(dtype):
             start_artifact = prep.artifact
-            youngest_artifact = prep.artifact.youngest_artifact
             info = {
                 'name': 'PREP %d NAME' % prep.id,
                 'id': prep.id,
                 'status': prep.status,
-                'start_artifact': start_artifact.artifact_type,
-                'start_artifact_id': start_artifact.id,
-                'youngest_artifact': ' - '.join(
-                    [youngest_artifact.name, youngest_artifact.artifact_type])
             }
+            if start_artifact is not None:
+                youngest_artifact = prep.artifact.youngest_artifact
+                info['start_artifact'] = start_artifact.artifact_type
+                info['start_artifact_id'] = start_artifact.id
+                info['youngest_artifact'] = '%s - %s' % (
+                    youngest_artifact.name, youngest_artifact.artifact_type)
+            else:
+                info['start_artifact'] = None
+                info['start_artifact_id'] = None
+                info['youngest_artifact'] = None
+
             prep_info[dtype].append(info)
     return {'status': 'success',
             'message': '',
-            'info': prep_info
-            }
+            'info': prep_info}

qiita_pet/handlers/api_proxy/tests/test_prep_template.py

@@ -25,10 +25,27 @@
     prep_template_put_req, prep_template_delete_req, prep_template_get_req,
     prep_template_graph_get_req, prep_template_filepaths_get_req,
     ena_ontology_get_req, _process_investigation_type,
-    _check_prep_template_exists)
+    _check_prep_template_exists, new_prep_template_get_req)
 
 
 class TestPrepAPIReadOnly(TestCase):
+    def test_new_prep_template_get_req(self):
+        obs = new_prep_template_get_req(1)
+        exp = {
+            'status': 'success',
+            'prep_files': ['uploaded_file.txt'],
+            'data_types': ['16S', '18S', 'ITS', 'Metabolomic', 'Metagenomic',
+                           'Proteomic'],
+            'ontology': {
+                'ENA': ['Cancer Genomics', 'Epigenetics', 'Exome Sequencing',
+                        'Forensic or Paleo-genomics', 'Gene Regulation Study',
+                        'Metagenomics', 'Pooled Clone Sequencing',
+                        'Population Genomics', 'RNASeq', 'Resequencing',
+                        'Synthetic Genomics', 'Transcriptome Analysis',
+                        'Whole Genome Sequencing', 'Other'],
+                'User': []}}
+        self.assertEqual(obs, exp)
+
     def test_check_prep_template_exists(self):
         obs = _check_prep_template_exists(1)
         self.assertEqual(obs, {'status': 'success', 'message': ''})
@@ -228,8 +245,9 @@ def setUp(self):
         with open(self.update_fp, 'w') as f:
             f.write("""sample_name\tnew_col\n1.SKD6.640190\tnew_value\n""")
 
-    def tear_down(self):
-        remove(self.update_fp)
+    def tearDown(self):
+        if exists(self.update_fp):
+            remove(self.update_fp)
 
         fp = join(get_mountpoint("uploads")[0][1], '1', 'uploaded_file.txt')
         if not exists(fp):

qiita_pet/handlers/prep_template.py

@@ -0,0 +1,30 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from tornado.web import authenticated
+
+from qiita_pet.handlers.base_handlers import BaseHandler
+from qiita_pet.handlers.api_proxy import prep_template_post_req
+
+
+class PrepTemplateHandler(BaseHandler):
+    @authenticated
+    def post(self):
+        """Creates a prep template"""
+        study_id = self.get_argument('study_id')
+        data_type = self.get_argument('data-type')
+        ena_ontology = self.get_argument('ena-ontology', None)
+        user_ontology = self.get_argument('user-ontology', None)
+        new_ontology = self.get_argument('new-ontology', None)
+        prep_fp = self.get_argument('prep-file')
+
+        response = prep_template_post_req(
+            study_id, self.get_current_user().id, prep_fp, data_type,
+            ena_ontology, user_ontology, new_ontology)
+
+        self.write(response)

qiita_pet/handlers/study_handlers/__init__.py

@@ -12,9 +12,11 @@
 from .description_handlers import PreprocessingSummaryHandler
 from .ebi_handlers import EBISubmitHandler
 from .vamps_handlers import VAMPSHandler
-from .base import StudyIndexHandler, StudyBaseInfoAJAX, StudyDeleteAjax
+from .base import (StudyIndexHandler, StudyBaseInfoAJAX, StudyDeleteAjax,
+                   DataTypesMenuAJAX)
 from .prep_template import (
-    PrepTemplateGraphAJAX, PrepTemplateAJAX, PrepFilesHandler)
+    PrepTemplateGraphAJAX, PrepTemplateAJAX, PrepFilesHandler,
+    NewPrepTemplateAjax)
 from .processing import (ProcessArtifactHandler, ListCommandsHandler,
                          ListOptionsHandler)
 from .artifact import (ArtifactGraphAJAX, NewArtifactHandler,
@@ -29,4 +31,5 @@
            'StudyBaseInfoAJAX', 'SampleTemplateAJAX', 'PrepTemplateAJAX',
            'NewArtifactHandler', 'PrepFilesHandler', 'ProcessArtifactHandler',
            'ListCommandsHandler', 'ListOptionsHandler', 'SampleAJAX',
-           'StudyDeleteAjax', 'ArtifactAJAX']
+           'StudyDeleteAjax', 'ArtifactAJAX', 'NewPrepTemplateAjax',
+           'DataTypesMenuAJAX']

qiita_pet/handlers/study_handlers/artifact.py

@@ -70,8 +70,8 @@ def post(self, study_id):
         artifact = artifact_post_req(
             self.current_user.id, files, artifact_type, name, prep['id'])
         if artifact['status'] == 'success' and prep['status'] != 'warning':
-                self.write({'status': 'success',
-                            'message': 'Artifact created successfully'})
+            self.write({'status': 'success',
+                        'message': 'Artifact created successfully'})
         else:
             self.write(prep)
 

qiita_pet/handlers/study_handlers/base.py

@@ -12,27 +12,23 @@
 from qiita_pet.handlers.util import to_int, doi_linkifier
 from qiita_pet.handlers.base_handlers import BaseHandler
 from qiita_pet.handlers.api_proxy import (
-    study_prep_get_req, data_types_get_req, study_get_req, study_delete_req)
+    study_prep_get_req, study_get_req, study_delete_req)
 
 
 class StudyIndexHandler(BaseHandler):
     @authenticated
     def get(self, study_id):
         study = to_int(study_id)
 
-        # Proxies for what will become API requests
-        prep_info = study_prep_get_req(study, self.current_user.id)
-        # Make sure study exists
-        if prep_info['status'] != 'success':
-            raise HTTPError(404, prep_info['message'])
+        study_info = study_get_req(study, self.current_user.id)
+        if study_info['status'] != 'success':
+            raise HTTPError(404, study_info['message'])
+
+        study_info = study_info['info']
 
-        prep_info = prep_info['info']
-        data_types = data_types_get_req()['data_types']
-        study_info = study_get_req(study, self.current_user.id)['info']
         editable = study_info['status'] == 'sandbox'
 
-        self.render("study_base.html", prep_info=prep_info,
-                    data_types=data_types, study_info=study_info,
+        self.render("study_base.html", study_info=study_info,
                     editable=editable)
 
 
@@ -57,3 +53,18 @@ class StudyDeleteAjax(BaseHandler):
     def post(self):
         study_id = self.get_argument('study_id')
         self.write(study_delete_req(int(study_id), self.current_user.id))
+
+
+class DataTypesMenuAJAX(BaseHandler):
+    @authenticated
+    def get(self):
+        study_id = to_int(self.get_argument('study_id'))
+        # Retrieve the prep template information for the menu
+        prep_info = study_prep_get_req(study_id, self.current_user.id)
+        # Make sure study exists
+        if prep_info['status'] != 'success':
+            raise HTTPError(404, prep_info['message'])
+
+        prep_info = prep_info['info']
+
+        self.render('study_ajax/data_type_menu.html', prep_info=prep_info)

qiita_pet/handlers/study_handlers/prep_template.py

@@ -20,7 +20,20 @@
     prep_template_summary_get_req, prep_template_post_req,
     prep_template_put_req, prep_template_delete_req,
     prep_template_filepaths_get_req, data_types_get_req,
-    prep_template_graph_get_req, ena_ontology_get_req)
+    prep_template_graph_get_req, ena_ontology_get_req,
+    new_prep_template_get_req)
+
+
+class NewPrepTemplateAjax(BaseHandler):
+    @authenticated
+    def get(self):
+        study_id = to_int(self.get_argument('study_id'))
+        result = new_prep_template_get_req(study_id)
+        self.render('study_ajax/add_prep_template.html',
+                    prep_files=result['prep_files'],
+                    data_types=result['data_types'],
+                    ontology=result['ontology'],
+                    study_id=study_id)
 
 
 class PrepTemplateGraphAJAX(BaseHandler):

qiita_pet/handlers/study_handlers/tests/test_base.py

@@ -38,5 +38,18 @@ def test_delete_study(self):
                           'erased because it has a sample template'}
         self.assertEqual(loads(response.body), exp)
 
+
+class DataTypesMenuAJAXTests(TestHandlerBase):
+    def test_get(self):
+        response = self.get('/study/description/data_type_menu/',
+                            {'study_id': '1'})
+        self.assertEqual(response.code, 200)
+        self.assertNotEqual(response.body, "")
+
+    def test_get_no_exists(self):
+        response = self.get('/study/description/data_type_menu/',
+                            {'study_id': '245'})
+        self.assertEqual(response.code, 404)
+
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_prep_template.py

@@ -12,6 +12,12 @@
 from qiita_db.ontology import Ontology
 
 
+class TestNewPrepTemplateAjax(TestHandlerBase):
+    def test_get(self):
+        response = self.get('/study/new_prep_template/', {'study_id': '1'})
+        self.assertEqual(response.code, 200)
+
+
 class TestPrepTemplateGraphAJAX(TestHandlerBase):
     def test_get(self):
         response = self.get('/prep/graph/', {'prep_id': 1})

qiita_pet/templates/study_ajax/add_prep_artifact.html

@@ -59,6 +59,7 @@
       $(ft+'-div').removeClass('highlight');
       $("#"+ft).val(files);
     }
+    return true;
   }
 
   $(document).ready(function () {
@@ -148,15 +149,15 @@ <h4>Select Investigation Type</h4>
           <option value="{{o}}">{{o}}</option>
         {% end %}
         </select></p>
-        <p id="user-ena-info"> User defined investigation type: 
+        <p id="user-ena-info"> User defined investigation type:
         <select id="user-ontology" name="user-ontology" value="user-ontology">
         <option value=""></option>
         {% for o in ontology['User'] %}
           <option value="{{o}}">{{o}}</option>
         {% end %}
         <option value="New Type">New Type</option>
         </select></p>
-        <p id="new-ena-info">New user defined term: 
+        <p id="new-ena-info">New user defined term:
         <input type="textbox" id="new-ontology" name="new-ontology"></p>
     </div>
     <div class="col-md-3">
@@ -184,7 +185,7 @@ <h4>Click and drag your files to the correct file subtype.</h4>
   </div>
   <div class="row" id="submit-div" hidden>
     <div class="col-md-12">
-      <button class="btn btn-sm btn-danger" onclick="fill_new_prep(); return false;">Reset</button> <input type="submit" class="btn btn-sm btn-success" value="Create New Preperation">
+      <button class="btn btn-sm btn-danger" onclick="fill_new_prep(); return false;">Reset</button> <input type="submit" class="btn btn-sm btn-success" value="Create New Preparation">
     </div>
   </div>
-</form>
+</form>