Delete study functionality

qiita_pet/handlers/api_proxy/__init__.py

@@ -22,7 +22,8 @@
     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)
-from .studies import data_types_get_req, study_get_req, study_prep_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
 
 __all__ = ['prep_template_summary_get_req', 'sample_template_post_req',
@@ -32,7 +33,7 @@
            'prep_template_summary_get_req', 'prep_template_post_req',
            'prep_template_put_req', 'prep_template_delete_req',
            'prep_template_graph_get_req', 'prep_template_filepaths_get_req',
-           'artifact_get_graph', 'prep_template_get_req',
+           'artifact_get_graph', 'prep_template_get_req', 'study_delete_req',
            'study_prep_get_req', 'sample_template_get_req',
            'artifact_graph_get_req', 'ena_ontology_get_req',
            'sample_template_meta_cats_get_req',

qiita_pet/handlers/api_proxy/studies.py

@@ -88,6 +88,40 @@ def study_get_req(study_id, user_id):
             }
 
 
+def study_delete_req(study_id, user_id):
+    """Delete a given study
+
+    Parameters
+    ----------
+    study_id : int
+        Study id to delete
+    user_id : str
+        User requesting the deletion
+
+    Returns
+    -------
+    dict
+        Status of deletion, in the format
+        {status: status,
+         message: message}
+    """
+    access_error = check_access(study_id, user_id)
+    if access_error:
+        return access_error
+
+    status = 'success'
+    try:
+        Study.delete(int(study_id))
+        msg = ''
+    except Exception as e:
+        status = 'error'
+        msg = 'Unable to delete study: %s' % str(e)
+    return {
+        'status': status,
+        'message': msg
+    }
+
+
 def study_prep_get_req(study_id, user_id):
     """Gives a summary of each prep template attached to the study
 

qiita_pet/handlers/api_proxy/tests/test_studies.py

@@ -8,10 +8,13 @@
 from unittest import TestCase, main
 from datetime import datetime
 
+from qiita_core.util import qiita_test_checker
+import qiita_db as qdb
 from qiita_pet.handlers.api_proxy.studies import (
-    data_types_get_req, study_get_req, study_prep_get_req)
+    data_types_get_req, study_get_req, study_prep_get_req, study_delete_req)
 
 
+@qiita_test_checker
 class TestStudyAPI(TestCase):
     def test_data_types_get_req(self):
         obs = data_types_get_req()
@@ -101,5 +104,49 @@ def test_study_prep_get_req_no_access(self):
                'message': 'User does not have access to study'}
         self.assertEqual(obs, exp)
 
+    def test_study_delete_req(self):
+        info = {
+            "timeseries_type_id": 1,
+            "metadata_complete": True,
+            "mixs_compliant": True,
+            "number_samples_collected": 25,
+            "number_samples_promised": 28,
+            "study_alias": "FCM",
+            "study_description": "DESC",
+            "study_abstract": "ABS",
+            "emp_person_id": qdb.study.StudyPerson(2),
+            "principal_investigator_id": qdb.study.StudyPerson(3),
+            "lab_person_id": qdb.study.StudyPerson(1)
+        }
+
+        new_study = qdb.study.Study.create(
+            qdb.user.User('test@foo.bar'), "Some New Study", [1],
+            info)
+
+        study_delete_req(new_study.id, 'test@foo.bar')
+
+        with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError):
+            qdb.study.Study(new_study.id)
+
+    def test_study_delete_req_error(self):
+        obs = study_delete_req(1, 'test@foo.bar')
+        exp = {'status': 'error',
+               'message': 'Unable to delete study: Study "Identification of '
+                          'the Microbiomes for Cannabis Soils" cannot be '
+                          'erased because it has a sample template'}
+        self.assertEqual(obs, exp)
+
+    def test_study_delete_req_no_access(self):
+        obs = study_delete_req(1, 'demo@microbio.me')
+        exp = {'status': 'error',
+               'message': 'User does not have access to study'}
+        self.assertEqual(obs, exp)
+
+    def test_study_delete_req_no_exists(self):
+        obs = study_delete_req(4, 'test@foo.bar')
+        exp = {'status': 'error',
+               'message': 'Study does not exist'}
+        self.assertEqual(obs, exp)
+
 if __name__ == '__main__':
     main()

qiita_pet/handlers/study_handlers/__init__.py

@@ -13,7 +13,7 @@
                                    PreprocessingSummaryHandler)
 from .ebi_handlers import EBISubmitHandler
 from .vamps_handlers import VAMPSHandler
-from .base import StudyIndexHandler, StudyBaseInfoAJAX
+from .base import StudyIndexHandler, StudyBaseInfoAJAX, StudyDeleteAjax
 from .prep_template import PrepTemplateGraphAJAX, PrepTemplateAJAX
 from .artifact import ArtifactGraphAJAX
 from .sample_template import SampleTemplateAJAX, SampleAJAX
@@ -24,4 +24,4 @@
            'MetadataSummaryHandler', 'VAMPSHandler', 'SearchStudiesAJAX',
            'PrepTemplateGraphAJAX', 'ArtifactGraphAJAX',
            'StudyIndexHandler', 'StudyBaseInfoAJAX', 'SampleTemplateAJAX',
-           'PrepTemplateAJAX', 'SampleAJAX']
+           'PrepTemplateAJAX', 'SampleAJAX', 'StudyDeleteAjax']

qiita_pet/handlers/study_handlers/base.py

@@ -12,7 +12,7 @@
 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_prep_get_req, data_types_get_req, study_get_req, study_delete_req)
 
 
 class StudyIndexHandler(BaseHandler):
@@ -51,3 +51,9 @@ def get(self):
         self.render('study_ajax/base_info.html',
                     study_info=study_info, publications=study_doi, pi=pi,
                     contact=contact)
+
+
+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))

qiita_pet/templates/study_base.html

@@ -25,7 +25,7 @@
         var nodes = [];
         // format edge list data
         for(i=0;i<data.edge_list.length;i++) {
-          edges.push({from: data.edge_list[i][0], to: data.edge_list[i][1],});
+          edges.push({from: data.edge_list[i][0], to: data.edge_list[i][1]});
         }
         //format node depth data
         for(i=0;i<data.node_labels.length;i++) {
@@ -35,12 +35,12 @@
         draw_graph(nodes, edges, "study-prep-graph");
         // Copy existing formatted prep info to header position
         $("#study-prep-subheader").html("<h2>" + $("#prep-header-" + pid).html() + '</h2><a href="#" onclick="togglegraphs(); return false;" id="graph-toggle-link">Hide files</a>');
-      });
-    $.get( "/study/description/prep_template/", { prep_id: pid, study_id: {{study_info['study_id']}}} )
+    });
+    $.get( "/study/description/prep_template/", { prep_id: pid, study_id: {{study_info['study_id']}} } )
       .done(function( data ) {
         $("#study-main").html(data);
-      });
-    }
+    });
+  }
 
   function draw_graph(nodes, edges, target) {
     var container = document.getElementById(target);
@@ -112,11 +112,37 @@
   $(document).ready(function() {
     fill_base({{study_info['study_id']}});
   });
+
+  function validate_delete_study_text() {
+    if ($("#study-alias").val() == "{{study_info['study_alias']}}") {
+      $('#delete-study-button').prop('disabled', false);
+    } else {
+      $('#delete-study-button').prop('disabled', true);
+    }
+  }
+
+function delete_study() {
+  if ($("#study-alias").val() != "{{study_info['study_alias']}}") {
+    alert("The entered study alias doesn't match the study");
+    return false;
+  }
+  if (confirm("Are you sure you want to delete {{study_info['study_title']}}?")) {
+    $.post('/study/delete/', {study_id: {{study_info['study_id']}}})
+      .done(function ( data ) {
+        if(data["status"] == "error") {
+          bootstrapAlert(data.message.replace("\n", "<br/>"), "danger", 4000);
+        } else {
+          window.location.replace = '/'
+        }
+      });
+  }
+}
 </script>
 <style>
 .graph {
   width:100%;
-  height:500px;
+  height:300px;
+  border: 1px solid #ccc;
 }
 </style>
 {% end %}
@@ -128,8 +154,8 @@ <h3><a href="#" onclick="fill_base({{study_info['study_id']}})">Study Informatio
     <a href="#" onclick="fill_sample_summary({{study_info['study_id']}}); return false;">Sample Summary</a><br />
     {% if editable %}
     <a href="/study/upload/{{study_info['study_id']}}">Upload Files</a><br />
-    <a href="#">Edit Study Information</a><br />
-    <a href="#">Delete Study</a>
+    <a href="/study/edit/{{study_info['study_id']}}">Edit Study Information</a><br />
+    <a href="#" data-toggle="modal" data-target="#delete-study">Delete Study</a>
     {% end %}
 
     <h3>Data Types</h3>
@@ -177,4 +203,23 @@ <h3>{{study_info['study_alias']}}</h3>
     <div class="row"><div class="col-md-12" id="study-main"></div></div>
   </div>
 </div>
+
+<div class="modal fade delete-study" tabindex="-1" role="dialog" id="delete-study">
+  <div class="modal-dialog modal-md">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button>
+        <h3>Deleting:<br/></h3><h4>{{study_info['study_title']}}</h4>
+      </div>
+      <div class="modal-body">
+        You will only be able to delete a study that has no data associated with it.
+      </div>
+      <div class="modal-footer">
+        To continue you need to write the alias name of the study:
+        <input type="text" name="study-alias" id="study-alias" onkeyup="validate_delete_study_text();">
+        <button class="btn btn-danger glyphicon glyphicon-trash" onclick="delete_study();" id="delete-study-button" disabled></button>
+      </div>
+    </div>
+  </div>
+</div>
 {% end %}

qiita_pet/test/test_study_handlers.py

@@ -646,6 +646,15 @@ def test_post_error(self):
 class TestDelete(TestHandlerBase):
     database = True
 
+    def test_delete_study(self):
+        response = self.post('/study/delete/', {'study_id': 1})
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'error',
+               'message': 'Unable to delete study: Study "Identification of '
+                          'the Microbiomes for Cannabis Soils" cannot be '
+                          'erased because it has a sample template'}
+        self.assertEqual(loads(response.body), exp)
+
     def test_delete_sample_template(self):
         response = self.post('/study/description/sample_template/',
                              {'study_id': 1,

qiita_pet/webserver.py

@@ -26,7 +26,7 @@
     StudyEditHandler, ListStudiesHandler, SearchStudiesAJAX, EBISubmitHandler,
     CreateStudyAJAX, ShareStudyAJAX, StudyApprovalList, ArtifactGraphAJAX,
     PreprocessingSummaryHandler, VAMPSHandler, PrepTemplateGraphAJAX,
-    PrepTemplateAJAX, SampleAJAX)
+    PrepTemplateAJAX, SampleAJAX, StudyDeleteAjax)
 from qiita_pet.handlers.websocket_handlers import (
     MessageHandler, SelectedSocketHandler, SelectSamplesHandler)
 from qiita_pet.handlers.logger_handlers import LogEntryViewerHandler
@@ -113,6 +113,7 @@ def __init__(self):
             (r"/study/description/prep_template/", PrepTemplateAJAX),
             (r"/study/description/baseinfo/", StudyBaseInfoAJAX),
             (r"/study/description/(.*)", StudyIndexHandler),
+            (r"/study/delete/", StudyDeleteAjax),
             (r"/study/upload/(.*)", StudyUploadFileHandler),
             (r"/upload/", UploadFileHandler),
             (r"/check_study/", CreateStudyAJAX),