Add duplicates and tube_ids feature draft 1

qiita-spots · May 19, 2023 · 5843087 · 5843087
1 parent f8cf31f
commit 5843087
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Showing 2 changed files with 46 additions and 8 deletions.
diff --git a/qiita_pet/handlers/admin_processing_job.py b/qiita_pet/handlers/admin_processing_job.py
@@ -105,28 +105,58 @@ def get(self):
 
     @execute_as_transaction
     def post(self):
-
-        # Get user-inputted qiita id and sample names
+        # Get user-inputted qiita id and sample names / tube_ids
         qid = self.get_argument("qid")
         snames = self.get_argument("snames").split()
 
+        # Get study give qiita id
+        st = Study(qid).sample_template
+
         # Stripping leading qiita id from sample names
         # Example: 1.SKB1.640202 -> SKB1.640202
-        qsnames = list(Study(qid).sample_template)
+        qsnames = list(st)
         for i, qsname in enumerate(qsnames):
             if qsname.startswith(qid):
                 qsnames[i] = qsname.replace(f'{qid}.', "", 1)
 
+        # Adds tube ids to a dict with key as tube id and value as qsname
+        tube_ids_dict = dict()
+        tube_ids_rev = dict()
+        tube_ids = set()
+        if "tube_id" in st.categories:
+            for qsname, tid in st.get_category("tube_id").items():
+                tube_ids.add(tid)
+                tube_ids_dict[qsname.replace(f'{qid}.', "", 1) if qsname.startswith(qid) else qsname] = tid
+                tube_ids_rev[tid] = qsname.replace(f'{qid}.', "", 1) if qsname.startswith(qid) else qsname
+
+        # Adds tube ids after sample name in paranthesis
+        if len(tube_ids) > 0:
+            for i, sname in enumerate(snames):
+                if sname in qsnames:
+                    snames[i] = f'{sname} ({tube_ids_dict[sname]})'
+                elif sname in tube_ids:
+                    snames[i] = f'{tube_ids_rev[sname]} ({sname})' 
+
+        # Finds duplicates in the samples
+        seen = dict()
+        for sample in snames:
+            if sample in seen:
+                seen[sample] += 1
+            else:
+                seen[sample] = 1
+
+        duplicates = set([f'{sample} \u00D7 {num}' for sample, num in seen.items() if num > 1])
+
         # Remove blank samples from sample names
-        blank = [x for x in snames if x.lower().startswith('blank')]
+        blank = set([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)
+        qsnames = set(qsnames) if len(tube_ids) == 0 else set([f'{x} ({tube_ids_dict[x]})' for x in 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, duplicates=duplicates)
diff --git a/qiita_pet/templates/sample_validation.html b/qiita_pet/templates/sample_validation.html
@@ -3,7 +3,7 @@
 <style>
     .column {
     float: left;
-    width: 25%;
+    width: 20%;
     }
 
     .row:after {
@@ -49,6 +49,14 @@ <h2>Blank</h2>
             {% end %}
         </ul>
     </div>
+    <div class="column">
+        <h2>Duplicates</h2>
+        <ul>
+            {% for sample in duplicates %}
+            <li>{{ sample }}</li>
+            {% end %}
+        </ul>
+    </div>
     <div class="column">
         <h2>Extra</h2>
         <ul>