Merge pull request #3294 from antgonza/fix-3227

fix #3227
qiita-spots · Jun 2, 2023 · fc17977 · fc17977
2 parents 87c2e51 + e159ee4
commit fc17977
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Showing 3 changed files with 37 additions and 23 deletions.
diff --git a/qiita_pet/handlers/admin_processing_job.py b/qiita_pet/handlers/admin_processing_job.py
@@ -14,6 +14,7 @@
 
 from qiita_db.software import Software
 from qiita_db.study import Study
+from qiita_db.exceptions import QiitaDBUnknownIDError
 
 from json import dumps
 
@@ -101,32 +102,39 @@ class SampleValidation(AdminProcessingJobBaseClass):
     def get(self):
         self._check_access()
 
-        self.render("sample_validation.html", input=True)
+        self.render("sample_validation.html", input=True, error=None)
 
     @execute_as_transaction
     def post(self):
-
         # Get user-inputted qiita id and sample names
         qid = self.get_argument("qid")
         snames = self.get_argument("snames").split()
+        error, matching, missing, extra, blank = [None]*5
 
         # Stripping leading qiita id from sample names
         # Example: 1.SKB1.640202 -> SKB1.640202
-        qsnames = list(Study(qid).sample_template)
-        for i, qsname in enumerate(qsnames):
-            if qsname.startswith(qid):
-                qsnames[i] = qsname.replace(f'{qid}.', "", 1)
-
-        # Remove blank samples from sample names
-        blank = [x for x in snames if x.lower().startswith('blank')]
-        snames = [x for x in snames if 'blank' not in x.lower()]
-
-        # Validate user's sample names against qiita study
-        qsnames = set(qsnames)
-        snames = set(snames)
-        matching = qsnames.intersection(snames)
-        missing = qsnames.difference(snames)
-        extra = snames.difference(qsnames)
+        try:
+            qsnames = list(Study(qid).sample_template)
+        except TypeError:
+            error = f'Study {qid} seems to have no sample template'
+        except QiitaDBUnknownIDError:
+            error = f'Study {qid} does not exist'
+
+        if error is None:
+            for i, qsname in enumerate(qsnames):
+                if qsname.startswith(qid):
+                    qsnames[i] = qsname.replace(f'{qid}.', "", 1)
+
+            # Remove blank samples from sample names
+            blank = [x for x in snames if x.lower().startswith('blank')]
+            snames = set(snames) - set(blank)
+
+            # Validate user's sample names against qiita study
+            qsnames = set(qsnames)
+            snames = set(snames)
+            matching = qsnames.intersection(snames)
+            missing = qsnames.difference(snames)
+            extra = snames.difference(qsnames)
 
         self.render("sample_validation.html", input=False, matching=matching,
-                    missing=missing, extra=extra, blank=blank)
+                    missing=missing, extra=extra, blank=blank, error=error)
diff --git a/qiita_pet/templates/sample_validation.html b/qiita_pet/templates/sample_validation.html
@@ -14,9 +14,13 @@
 </style>
 {% end %}
 {% block content %}
-<h1>Sample Validation</h1><br>
-{% if input %}
-<form action="{% raw qiita_config.portal_dir %}/admin/sample_validation/" method="post" id="sample_validation_form"> 
+{% if input or error is not None %}
+  {% if error is not None %}
+    <div class="alert alert-danger" role="alert">
+      {{error}}
+    </div>
+  {% end %}
+<form action="{% raw qiita_config.portal_dir %}/admin/sample_validation/" method="post" id="sample_validation_form">
     <label for="qid">Qiita id:</label><br>
     <input type="text" id="qid" name="qid"><br>
     <label for="snames">Sample names:</label><br>
@@ -32,7 +36,7 @@ <h2>Matching</h2>
             <li>{{ sample }}</li>
             {% end %}
         </ul>
-    </div> 
+    </div>
     <div class="column">
         <h2>Missing</h2>
         <ul>

diff --git a/qiita_pet/test/test_admin_processing_job_handlers.py b/qiita_pet/test/test_admin_processing_job_handlers.py
@@ -62,13 +62,15 @@ def test_post(self):
         body = response.body.decode('ascii')
         for name in snames:
             self.assertIn(name, body)
+
         # Check failure: invalid qiita id
         post_args = {
             'qid': 2,
             'snames': 'SKB1.640202 SKB2.640194 BLANK.1A BLANK.1B'
         }
         response = self.post('/admin/sample_validation/', post_args)
-        self.assertEqual(response.code, 500)
+        self.assertEqual(response.code, 200)
+        self.assertIn('Study 2 does not exist', response.body.decode('ascii'))
 
 
 if __name__ == "__main__":