Added prep_id as an optional parameter (#3262)

* Added prep_id as an optional parameter

Added prep_id as an optional parameter to
.../study/description/<study_id>?prep_id=<prep_id>.

This will bring up the prep_id workflow page instead of summary
information.

* Temporarily removing CA check for QIIME2 download

* Added error-checking

Author: charles-cowart

qiita_pet/handlers/study_handlers/base.py

@@ -23,6 +23,7 @@ def get(self, study_id):
         study = to_int(study_id)
         level = self.get_argument('level', '')
         message = self.get_argument('message', '')
+        prep_id = self.get_argument('prep_id', default=None)
 
         study_info = study_get_req(study, self.current_user.id)
         if study_info['status'] != 'success':
@@ -32,6 +33,25 @@ def get(self, study_id):
             study_info['level'] = level
             study_info['message'] = message
 
+        if prep_id:
+            msg = f"'{prep_id}' is not a valid preparation for this study"
+            study_info['study_info']['prep_id'] = to_int(prep_id, msg)
+
+            # prep_id is an integer - confirm that it's a valid prep_id.
+            prep_info = study_prep_get_req(study, self.current_user.id)
+            if prep_info['status'] != 'success':
+                raise HTTPError(404, reason=prep_info['message'])
+
+            prep_ids = []
+            for prep_type in prep_info['info']:
+                # prep_type will be either '18S', '16S', or similarly named.
+                # generate a list of prep-ids from the preps in each list.
+                prep_ids += [x['id'] for x in prep_info['info'][prep_type]]
+
+            if study_info['study_info']['prep_id'] not in prep_ids:
+                raise HTTPError(400, reason=(f"'{prep_id}' is not a valid "
+                                             "preparation for this study"))
+
         self.render("study_base.html", **study_info)
 
 

qiita_pet/handlers/study_handlers/tests/test_base.py

@@ -17,11 +17,18 @@ class StudyIndexHandlerTests(TestHandlerBase):
     def test_get_exists(self):
         response = self.get('/study/description/1')
         self.assertEqual(response.code, 200)
+        self.assertTrue('study/description/baseinfo' in str(response.body))
 
     def test_get_no_exists(self):
         response = self.get('/study/description/245')
         self.assertEqual(response.code, 404)
 
+    def test_get_prep_page(self):
+        response = self.get('/study/description/1?prep_id=1')
+        self.assertEqual(response.code, 200)
+        self.assertTrue('study/description/prep_template' in
+                        str(response.body))
+
 
 class StudyBaseInfoAJAX(TestHandlerBase):
     # TODO: Missing tests

qiita_pet/handlers/util.py

@@ -81,7 +81,7 @@ def download_link_or_path(is_local_request, filepath, fp_id, label):
     linkify, "<a target=\"_blank\" href=\"http://dx.doi.org/{0}\">{0}</a>")
 
 
-def to_int(value):
+def to_int(value, reason=None):
     """Transforms `value` to an integer
 
     Parameters
@@ -102,8 +102,9 @@ def to_int(value):
     try:
         res = int(value)
     except ValueError:
-        raise HTTPError(400, reason="%s cannot be converted to an "
-                        "integer" % value)
+        msg = f"{value} cannot be converted to an integer" if reason is None \
+              else reason
+        raise HTTPError(400, reason=msg)
     return res
 
 

qiita_pet/templates/study_base.html

@@ -64,7 +64,11 @@
     // Populate the different sections of the page
     populate_data_type_menu_div();
     // The initial page to be shown is the base information of the study
-    populate_main_div("{% raw qiita_config.portal_dir %}/study/description/baseinfo/", { study_id: {{study_info['study_id']}}});
+    {% if 'prep_id' in study_info %}
+        populate_main_div("{% raw qiita_config.portal_dir %}/study/description/prep_template/", { prep_id: {{study_info['prep_id']}}, study_id: {{study_info['study_id']}}});
+    {% else %}
+        populate_main_div("{% raw qiita_config.portal_dir %}/study/description/baseinfo/", { study_id: {{study_info['study_id']}}});
+    {% end %}
 
     {% if study_info['num_samples'] > 0 %}
       $("#sample-summary-btn").show();