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sarayupaisarayupai
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add sample validation page for wetlab (#3213)
* add sample validation page for wetlab * add unit tests for sample validation page * address comments * add comments to sample validation tests * address flake8 feedback
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‎qiita_pet/handlers/admin_processing_job.py‎

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@@ -13,6 +13,7 @@
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from qiita_core.util import execute_as_transaction
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from qiita_db.software import Software
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from qiita_db.study import Study
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from json import dumps
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@@ -91,3 +92,40 @@ def get(self):
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# return the json in compact form to save transmit size
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self.write(dumps(results, separators=(',', ':')))
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class SampleValidation(AdminProcessingJobBaseClass):
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@coroutine
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@execute_as_transaction
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def get(self):
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self._check_access()
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self.render("sample_validation.html", input=True)
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@execute_as_transaction
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def post(self):
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# Get user-inputted qiita id and sample names
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qid = self.get_argument("qid")
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snames = self.get_argument("snames").split()
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# Stripping leading qiita id from sample names
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# Example: 1.SKB1.640202 -> SKB1.640202
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qsnames = list(Study(qid).sample_template)
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for i, qsname in enumerate(qsnames):
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if qsname.startswith(qid):
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qsnames[i] = qsname.replace(f'{qid}.', "", 1)
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# Remove blank samples from sample names
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blank = [x for x in snames if x.lower().startswith('blank')]
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snames = [x for x in snames if 'blank' not in x.lower()]
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# Validate user's sample names against qiita study
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qsnames = set(qsnames)
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snames = set(snames)
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matching = qsnames.intersection(snames)
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missing = qsnames.difference(snames)
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extra = snames.difference(qsnames)
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self.render("sample_validation.html", input=False, matching=matching,
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missing=missing, extra=extra, blank=blank)

‎qiita_pet/templates/sample_validation.html‎

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{% extends sitebase.html %}
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{% block head %}
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<style>
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.column {
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float: left;
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width: 25%;
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}
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.row:after {
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content: "";
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display: table;
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clear: both;
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}
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</style>
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{% end %}
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{% block content %}
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<h1>Sample Validation</h1><br>
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{% if input %}
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<form action="{% raw qiita_config.portal_dir %}/admin/sample_validation/" method="post" id="sample_validation_form">
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<label for="qid">Qiita id:</label><br>
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<input type="text" id="qid" name="qid"><br>
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<label for="snames">Sample names:</label><br>
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<textarea id="sname" name="snames"></textarea><br><br>
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<input type="submit" value="Submit">
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</form>
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{% else %}
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<div class="row">
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<div class="column">
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<h2>Matching</h2>
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<ul>
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{% for sample in matching %}
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<li>{{ sample }}</li>
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{% end %}
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</ul>
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</div>
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<div class="column">
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<h2>Missing</h2>
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<ul>
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{% for sample in missing %}
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<li>{{ sample }}</li>
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{% end %}
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</ul>
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</div>
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<div class="column">
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<h2>Blank</h2>
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<ul>
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{% for sample in blank %}
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<li>{{ sample }}</li>
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{% end %}
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</ul>
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</div>
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<div class="column">
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<h2>Extra</h2>
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<ul>
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{% for sample in extra %}
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<li>{{ sample }}</li>
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{% end %}
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</ul>
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</div>
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</div>
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<form action="{% raw qiita_config.portal_dir %}/admin/sample_validation/" method="get" id="return_to_sample_validation_form">
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<input type="submit" value="Validate more samples">
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</form>
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{% end %}
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{% end %}

‎qiita_pet/templates/sitebase.html‎

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

‎qiita_pet/test/test_admin_processing_job_handlers.py‎

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@@ -45,5 +45,31 @@ def test_get_missing_argument(self):
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response.body.decode('ascii'))
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class TestSampleValidation(BaseAdminTests):
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def test_get(self):
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response = self.get('/admin/sample_validation/')
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self.assertEqual(response.code, 200)
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def test_post(self):
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# Check success
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post_args = {
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'qid': 1,
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'snames': 'SKB1.640202 SKB2.640194 BLANK.1A BLANK.1B'
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}
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response = self.post('/admin/sample_validation/', post_args)
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self.assertEqual(response.code, 200)
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snames = ['SKB1.640202', 'SKB2.640194', 'BLANK.1A', 'BLANK.1B']
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body = response.body.decode('ascii')
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for name in snames:
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self.assertIn(name, body)
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# Check failure: invalid qiita id
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post_args = {
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'qid': 2,
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'snames': 'SKB1.640202 SKB2.640194 BLANK.1A BLANK.1B'
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}
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response = self.post('/admin/sample_validation/', post_args)
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self.assertEqual(response.code, 500)
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if __name__ == "__main__":
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main()

‎qiita_pet/webserver.py‎

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ChangeForgotPasswordHandler, ForgotPasswordHandler, UserProfileHandler,
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UserMessagesHander, UserJobs)
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from qiita_pet.handlers.admin_processing_job import (
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AdminProcessingJob, AJAXAdminProcessingJobListing)
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AdminProcessingJob, AJAXAdminProcessingJobListing, SampleValidation)
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from qiita_pet.handlers.analysis_handlers import (
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ListAnalysesHandler, AnalysisSummaryAJAX, SelectedSamplesHandler,
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AnalysisDescriptionHandler, AnalysisGraphHandler, CreateAnalysisHandler,
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(r"/admin/artifact/", ArtifactAdminAJAX),
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(r"/admin/processing_jobs/", AdminProcessingJob),
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(r"/admin/processing_jobs/list", AJAXAdminProcessingJobListing),
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(r"/admin/sample_validation/", SampleValidation),
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(r"/ebi_submission/(.*)", EBISubmitHandler),
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# Study handlers
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(r"/study/create/", StudyEditHandler),

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