add sample validation page for wetlab

qiita_pet/handlers/admin_processing_job.py

@@ -13,6 +13,7 @@
 from qiita_core.util import execute_as_transaction
 
 from qiita_db.software import Software
+from qiita_db.study import Study
 
 from json import dumps
 
@@ -91,3 +92,40 @@ def get(self):
 
         # return the json in compact form to save transmit size
         self.write(dumps(results, separators=(',', ':')))
+
+
+class SampleValidation(AdminProcessingJobBaseClass):
+    @coroutine
+    @execute_as_transaction
+    def get(self):
+        self._check_access()
+
+        self.render("sample_validation.html", input=True)
+
+    @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()
+
+        # 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)
+
+        self.render("sample_validation.html", input=False, matching=matching,
+                    missing=missing, extra=extra, blank=blank)

qiita_pet/templates/sample_validation.html

@@ -0,0 +1,65 @@
+{% extends sitebase.html %}
+{% block head %}
+<style>
+    .column {
+    float: left;
+    width: 25%;
+    }
+
+    .row:after {
+    content: "";
+    display: table;
+    clear: both;
+    }
+</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"> 
+    <label for="qid">Qiita id:</label><br>
+    <input type="text" id="qid" name="qid"><br>
+    <label for="snames">Sample names:</label><br>
+    <textarea id="sname" name="snames"></textarea><br><br>
+    <input type="submit" value="Submit">
+</form>
+{% else %}
+<div class="row">
+    <div class="column">
+        <h2>Matching</h2>
+        <ul>
+            {% for sample in matching %}
+            <li>{{ sample }}</li>
+            {% end %}
+        </ul>
+    </div> 
+    <div class="column">
+        <h2>Missing</h2>
+        <ul>
+            {% for sample in missing %}
+            <li>{{ sample }}</li>
+            {% end %}
+        </ul>
+    </div>
+    <div class="column">
+        <h2>Blank</h2>
+        <ul>
+            {% for sample in blank %}
+            <li>{{ sample }}</li>
+            {% end %}
+        </ul>
+    </div>
+    <div class="column">
+        <h2>Extra</h2>
+        <ul>
+            {% for sample in extra %}
+            <li>{{ sample }}</li>
+            {% end %}
+        </ul>
+    </div>
+</div>
+<form action="{% raw qiita_config.portal_dir %}/admin/sample_validation/" method="get" id="return_to_sample_validation_form">
+    <input type="submit" value="Validate more samples">
+</form>
+{% end %}
+{% end %}

qiita_pet/templates/sitebase.html

@@ -383,6 +383,7 @@
                       <li><a href="{% raw qiita_config.portal_dir %}/admin/error/">View Errors</a></li>
                       <li><a href="{% raw qiita_config.portal_dir %}/admin/approval/">View Studies awaiting approval</a></li>
                       <li><a href="{% raw qiita_config.portal_dir %}/admin/portals/studies/">Edit study portal connections</a></li>
+                      <li><a href="{% raw qiita_config.portal_dir %}/admin/sample_validation/">Sample Validation</a></li>
                     {% end %}
                     <li><a href="{% raw qiita_config.portal_dir %}/admin/processing_jobs/">Processing Jobs</a></li>
                   {% else %}

qiita_pet/test/test_admin_processing_job_handlers.py

@@ -45,5 +45,31 @@ def test_get_missing_argument(self):
                       response.body.decode('ascii'))
 
 
+class TestSampleValidation(BaseAdminTests):
+    def test_get(self):
+        response = self.get('/admin/sample_validation/')
+        self.assertEqual(response.code, 200)
+
+    def test_post(self):
+        # Check success
+        post_args = {
+            'qid': 1,
+            'snames': 'SKB1.640202 SKB2.640194 BLANK.1A BLANK.1B'
+        }
+        response = self.post('/admin/sample_validation/', post_args)
+        self.assertEqual(response.code, 200)
+        snames = ['SKB1.640202', 'SKB2.640194', 'BLANK.1A', 'BLANK.1B']
+        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)
+
+
 if __name__ == "__main__":
     main()

qiita_pet/webserver.py

@@ -25,7 +25,7 @@
     ChangeForgotPasswordHandler, ForgotPasswordHandler, UserProfileHandler,
     UserMessagesHander, UserJobs)
 from qiita_pet.handlers.admin_processing_job import (
-    AdminProcessingJob, AJAXAdminProcessingJobListing)
+    AdminProcessingJob, AJAXAdminProcessingJobListing, SampleValidation)
 from qiita_pet.handlers.analysis_handlers import (
     ListAnalysesHandler, AnalysisSummaryAJAX, SelectedSamplesHandler,
     AnalysisDescriptionHandler, AnalysisGraphHandler, CreateAnalysisHandler,
@@ -133,6 +133,7 @@ def __init__(self):
             (r"/admin/artifact/", ArtifactAdminAJAX),
             (r"/admin/processing_jobs/", AdminProcessingJob),
             (r"/admin/processing_jobs/list", AJAXAdminProcessingJobListing),
+            (r"/admin/sample_validation/", SampleValidation),
             (r"/ebi_submission/(.*)", EBISubmitHandler),
             # Study handlers
             (r"/study/create/", StudyEditHandler),