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Fix 1783: display EBI values #1804

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Merged
merged 2 commits into from
Apr 20, 2016
Merged

Fix 1783: display EBI values #1804

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b945511
fix #1783
antgonza Apr 19, 2016
854af66
add ebi to prep
antgonza Apr 19, 2016
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1 change: 1 addition & 0 deletions qiita_pet/handlers/api_proxy/prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,6 +180,7 @@ def prep_template_ajax_get_req(user_id, prep_id):
'editable': editable,
'data_type': pt.data_type(),
'alert_type': alert_type,
'ebi_experiment_accessions': pt.ebi_experiment_accessions,
'alert_message': alert_msg}


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2 changes: 2 additions & 0 deletions qiita_pet/handlers/api_proxy/studies.py
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Expand Up @@ -73,6 +73,8 @@ def study_get_req(study_id, user_id):
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status

# Clean up StudyPerson objects to string for display
pi = study_info['principal_investigator']
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27 changes: 27 additions & 0 deletions qiita_pet/handlers/api_proxy/tests/test_prep_template.py
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Expand Up @@ -88,6 +88,33 @@ def test_prep_template_ajax_get_req(self):
'editable': True,
'data_type': '18S',
'alert_type': '',
'ebi_experiment_accessions': {'1.SKB1.640202': 'ERX0000011',
'1.SKB2.640194': 'ERX0000008',
'1.SKB3.640195': 'ERX0000024',
'1.SKB4.640189': 'ERX0000020',
'1.SKB5.640181': 'ERX0000006',
'1.SKB6.640176': 'ERX0000025',
'1.SKB7.640196': 'ERX0000002',
'1.SKB8.640193': 'ERX0000000',
'1.SKB9.640200': 'ERX0000016',
'1.SKD1.640179': 'ERX0000012',
'1.SKD2.640178': 'ERX0000009',
'1.SKD3.640198': 'ERX0000013',
'1.SKD4.640185': 'ERX0000023',
'1.SKD5.640186': 'ERX0000017',
'1.SKD6.640190': 'ERX0000007',
'1.SKD7.640191': 'ERX0000021',
'1.SKD8.640184': 'ERX0000001',
'1.SKD9.640182': 'ERX0000019',
'1.SKM1.640183': 'ERX0000026',
'1.SKM2.640199': 'ERX0000015',
'1.SKM3.640197': 'ERX0000018',
'1.SKM4.640180': 'ERX0000004',
'1.SKM5.640177': 'ERX0000005',
'1.SKM6.640187': 'ERX0000022',
'1.SKM7.640188': 'ERX0000010',
'1.SKM8.640201': 'ERX0000014',
'1.SKM9.640192': 'ERX0000003'},
'alert_message': ''}
self.assertEqual(obs, exp)

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4 changes: 3 additions & 1 deletion qiita_pet/handlers/api_proxy/tests/test_studies.py
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Expand Up @@ -75,7 +75,9 @@ def test_study_get_req(self):
'study_title': 'Identification of the Microbiomes for '
'Cannabis Soils',
'number_samples_collected': 27,
'owner': 'test@foo.bar'},
'owner': 'test@foo.bar',
'ebi_submission_status': 'submitted',
'ebi_study_accession': 'EBI123456-BB'},
'editable': True}

self.assertEqual(obs, exp)
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9 changes: 8 additions & 1 deletion qiita_pet/handlers/study_handlers/base.py
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Expand Up @@ -46,10 +46,17 @@ def get(self):
share_access = (self.current_user.id in study_info['shared_with'] or
self.current_user.id == study_info['owner'])

ebi_info = study_info['ebi_submission_status']
if ebi_info == 'submitted':
ebi_info = ''.join([
('<a href="https://www.ebi.ac.uk/ena/data/view/{0}">{0}'
'</a></br>'.format(acc))
for acc in study_info['ebi_study_accession'].split(',')])

self.render('study_ajax/base_info.html',
study_info=study_info, publications=study_doi, pi=pi,
contact=contact, editable=res['editable'],
share_access=share_access)
share_access=share_access, ebi_info=ebi_info)


class StudyDeleteAjax(BaseHandler):
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2 changes: 2 additions & 0 deletions qiita_pet/templates/study_ajax/base_info.html
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Expand Up @@ -18,6 +18,8 @@
Shared With: <span id="shared_html_{{study_info['study_id']}}">
</span><br/>
Samples: {{study_info['num_samples']}}<br />
EBI: {% raw ebi_info %}<br />

{% if share_access %}
<a class="btn btn-default" data-toggle="modal" data-target="#share-study-modal-view" onclick="modify_sharing({{study_info['study_id']}});"><span class="glyphicon glyphicon-share"></span> Share</a>
{% end %}
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9 changes: 6 additions & 3 deletions qiita_pet/templates/study_ajax/prep_summary.html
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Expand Up @@ -353,7 +353,10 @@ <h4>
<!-- #samples and #columns -->
<div class="row">
<div class="col-md-12">
There are <b>{{num_samples}}</b> samples and <b>{{num_columns}}</b> columns in this preparation.
There are <b>{{num_samples}}</b> samples and <b>{{num_columns}}</b> columns in this preparation.</br>
{% if ebi_experiment_accessions %}
<b>EBI status: </b> Submitted
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We have other statuses available right? Any reason why we are not showing the current status instead of just Submitted?

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Not really, this is for preps. This is, the study is what's being submitted/updated and the prep is only submitted/not-submitted and we know is submitted if the samples have ebi_experiment_accessions.

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Got it.

On (Apr-20-16| 9:36), Antonio Gonzalez wrote:

@@ -353,7 +353,10 @@

- There are {{num_samples}} samples and {{num_columns}} columns in this preparation. - There are {{num_samples}} samples and {{num_columns}} columns in this preparation.
- {% if ebi_experiment_accessions %} - EBI status: Submitted

Not really, this is for preps. This is, the study is what's being submitted/updated and the prep is only submitted/not-submitted and we know is submitted if the samples have ebi_experiment_accessions.

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{% end %}
</div>
</div>

Expand Down Expand Up @@ -406,12 +409,12 @@ <h4>

<!-- Files graph or add artifact -->
<div class="row">
<div class="col-md-12" id="graph-or-new-artifact-div">
<div class="col-md-10" id="graph-or-new-artifact-div">
</div>
</div>

<!-- Prep information summary -->
<div class="row">
<div class="col-md-12" id="prep-artifact-summary-div">
<div class="col-md-10" id="prep-artifact-summary-div">
</div>
</div>