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Merged
antgonza merged 10 commits into from
Jun 18, 2021
Merged

fix #3054 #3115

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6d76f42
disable "Add Files" button after click (#3111)
antgonza May 28, 2021
acfff95
fix #3101
antgonza May 27, 2021
728b951
fix errors
antgonza May 28, 2021
c9cff26
deleting problematic study
antgonza May 28, 2021
7732491
fix error
antgonza May 28, 2021
451c7e0
@wasade review
antgonza May 28, 2021
9efe639
fix #3095
antgonza May 28, 2021
b19b52e
fix 3054 ("Improve preparation tab in GUI")
AmandaBirmingham Jun 16, 2021
944086c
Merge branch 'dev' of https://github.com/biocore/qiita into dev
AmandaBirmingham Jun 16, 2021
b00bfa6
code review changes
AmandaBirmingham Jun 18, 2021
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18 changes: 16 additions & 2 deletions qiita_pet/handlers/api_proxy/studies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,6 +206,7 @@ def study_prep_get_req(study_id, user_id):
prep_info = defaultdict(list)
editable = study.can_edit(User(user_id))
for dtype in study.data_types:
dtype_infos = list()
for prep in study.prep_templates(dtype):
if prep.status != 'public' and not editable:
continue
Expand All @@ -214,11 +215,18 @@ def study_prep_get_req(study_id, user_id):
'name': prep.name,
'id': prep.id,
'status': prep.status,
'total_samples': len(prep),
'creation_timestamp': prep.creation_timestamp,
'modification_timestamp': prep.modification_timestamp
}
if start_artifact is not None:
youngest_artifact = prep.artifact.youngest_artifact
info['start_artifact'] = start_artifact.artifact_type
info['start_artifact_id'] = start_artifact.id
info['num_artifact_children'] = len(start_artifact.children)
info['youngest_artifact_name'] = youngest_artifact.name
info['youngest_artifact_type'] = \
youngest_artifact.artifact_type
info['youngest_artifact'] = '%s - %s' % (
youngest_artifact.name, youngest_artifact.artifact_type)
info['ebi_experiment'] = len(
Expand All @@ -228,9 +236,15 @@ def study_prep_get_req(study_id, user_id):
info['start_artifact'] = None
info['start_artifact_id'] = None
info['youngest_artifact'] = None
info['ebi_experiment'] = False
info['ebi_experiment'] = 0

prep_info[dtype].append(info)
dtype_infos.append(info)

# default sort is in ascending order of creation timestamp
sorted_info = sorted(dtype_infos,
key=lambda k: k['creation_timestamp'],
reverse=False)
prep_info[dtype] = sorted_info

return {'status': 'success',
'message': '',
Expand Down
133 changes: 79 additions & 54 deletions qiita_pet/handlers/api_proxy/tests/test_studies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
from os import remove
from shutil import rmtree
from tempfile import mkdtemp
from collections import defaultdict

import pandas as pd
import numpy.testing as npt
Expand Down Expand Up @@ -228,15 +229,19 @@ def test_study_prep_get_req_failed_EBI(self):

# actual test
obs = study_prep_get_req(study.id, user_email)
temp_info = defaultdict(list)
temp_info['16S'] = [
{"status": 'sandbox',
'name': 'Prep information %d' % pt.id,
'start_artifact': None, 'youngest_artifact': None,
'ebi_experiment': False, 'id': pt.id,
'start_artifact_id': None,
'creation_timestamp': pt.creation_timestamp,
'modification_timestamp': pt.modification_timestamp,
'total_samples': 3}]

exp = {
'info': {
'16S': [
{'status': 'sandbox',
'name': 'Prep information %d' % pt.id,
'start_artifact': None, 'youngest_artifact': None,
'ebi_experiment': False, 'id': pt.id,
'start_artifact_id': None}]
},
'info': temp_info,
'message': '',
'status': 'success'}
self.assertEqual(obs, exp)
Expand Down Expand Up @@ -516,24 +521,43 @@ class TestStudyAPI2(TestStudyAPI):
# This test expects a clean DB so creating it's own class
def test_study_prep_get_req(self):
obs = study_prep_get_req(1, 'test@foo.bar')
obs_info = obs['info']['18S']
temp_info = defaultdict(list)
temp_info['18S'] = [{
'id': 1,
'status': 'private',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'youngest_artifact_name': 'BIOM',
'youngest_artifact_type': 'BIOM',
'num_artifact_children': 2,
'total_samples': 27,
'ebi_experiment': 27,
'modification_timestamp':
obs_info[0]['modification_timestamp'],
'creation_timestamp':
obs_info[0]['creation_timestamp']}, {
'id': 2,
'status': 'private',
'name': 'Prep information 2',
'start_artifact': 'BIOM',
'youngest_artifact': 'BIOM - BIOM',
'youngest_artifact_name': 'BIOM',
'youngest_artifact_type': 'BIOM',
'total_samples': 27,
'num_artifact_children': 0,
'ebi_experiment': 27,
'start_artifact_id': 7,
'modification_timestamp':
obs_info[1]['modification_timestamp'],
'creation_timestamp':
obs_info[1]['creation_timestamp']
}]
exp = {'status': 'success',
'message': '',
'info': {
'18S': [{
'id': 1,
'status': 'private',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27}, {
'id': 2,
'status': 'private',
'name': 'Prep information 2',
'start_artifact': 'BIOM',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27,
'start_artifact_id': 7}]}}
'info': temp_info}
self.assertEqual(obs, exp)

# Add a new prep template
Expand All @@ -543,47 +567,48 @@ def test_study_prep_get_req(self):
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}),
qdb.study.Study(1), '16S')
obs = study_prep_get_req(1, 'test@foo.bar')
temp_info['16S'] = [{'id': pt.id,
'status': 'sandbox',
'name': 'Prep information %d' % pt.id,
'creation_timestamp': pt.creation_timestamp,
'modification_timestamp':
pt.modification_timestamp,
'total_samples': 1,
'start_artifact_id': None,
'start_artifact': None,
'youngest_artifact': None,
'ebi_experiment': 0}]
exp = {'status': 'success',
'message': '',
'info': {
'18S': [{'id': 1,
'status': 'private',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27},
{'id': 2,
'status': 'private',
'name': 'Prep information 2',
'start_artifact_id': 7,
'start_artifact': 'BIOM',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27}],
'16S': [{'id': pt.id,
'status': 'sandbox',
'name': 'Prep information %d' % pt.id,
'start_artifact_id': None,
'start_artifact': None,
'youngest_artifact': None,
'ebi_experiment': 0}]}}
'info': temp_info}
self.assertEqual(obs, exp)

obs = study_prep_get_req(1, 'admin@foo.bar')
self.assertEqual(obs, exp)

qdb.artifact.Artifact(1).visibility = 'public'
obs = study_prep_get_req(1, 'demo@microbio.me')
temp_info = defaultdict(list)
temp_info['18S'] = [{
'id': 1,
'status': 'public',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'youngest_artifact_name': 'BIOM',
'youngest_artifact_type': 'BIOM',
'num_artifact_children': 2,
'total_samples': 27,
'ebi_experiment': 27,
'modification_timestamp':
obs_info[0]['modification_timestamp'],
'creation_timestamp':
obs_info[0]['creation_timestamp']}]
temp_info['16S'] = []
exp = {'status': 'success',
'message': '',
'info': {
'18S': [{'id': 1,
'status': 'public',
'name': 'Prep information 1',
'start_artifact_id': 1,
'start_artifact': 'FASTQ',
'youngest_artifact': 'BIOM - BIOM',
'ebi_experiment': 27}]}}
'info': temp_info}
self.assertEqual(obs, exp)
# Reset visibility of the artifacts
for i in range(4, 0, -1):
Expand Down
24 changes: 18 additions & 6 deletions qiita_pet/templates/study_ajax/data_type_menu.html
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Original file line number Diff line number Diff line change
@@ -1,5 +1,16 @@
{% from qiita_core.qiita_settings import qiita_config %}

<style>
.green {
color: green;
}

.red {
color: red;
}
</style>


<script type="text/javascript">
function toggle_color_prep(div){
div.parent().children().each(function() {
Expand All @@ -9,6 +20,8 @@
}
</script>

<!-- <script src="https://use.fontawesome.com/0c9cdb020f.js"></script> -->

{% if prep_info %}
<h3>Data Types <small>(click on the tabs)</small></h3>
<div class="panel-group" id="accordion" role="tablist" aria-multiselectable="true">
Expand All @@ -27,15 +40,14 @@ <h4 class="panel-title">
<div class="panel-body" style="padding: 0px 0px 0px 0px; border: none;">
{% for prep in prep_info[dt] %}
<div class="panel-body-element" style="padding: 20px 20px 20px 20px;">
{% if prep['ebi_experiment'] %}
<img src="{% raw qiita_config.portal_dir %}/static/img/ena.png" style="width:20px;height:20px;"> ({{prep['ebi_experiment']}})
{% end %}
Samples: {{ prep['total_samples'] }}{% if prep['ebi_experiment'] %}, <img src="{% raw qiita_config.portal_dir %}/static/img/ena.png" style="width:20px;height:20px;"> {{prep['ebi_experiment']}} {% end %}
<a href="#" style="display:block;color:black;" onclick="toggle_color_prep($(this).parent()); populate_main_div('{% raw qiita_config.portal_dir %}/study/description/prep_template/', { prep_id: {{prep['id']}}, study_id: {{study_id}} });">
<span id="prep-header-{{prep['id']}}">
{{prep['name']}} - ID {{prep['id']}} - {{prep['status']}}
{{prep['name']}} - ID: {{prep['id']}} - {{prep['status']}}
</span><br/>
{{prep['start_artifact']}} - ID {{prep['start_artifact_id']}}<br/>
{{prep['youngest_artifact']}}
Raw files {% if prep['start_artifact'] == 'FASTQ' %}<i class="fa fa-check green"></i>{% else %}<i class="fa fa-times red"></i>{% end %}, processed {% if prep['num_artifact_children'] > 0 %}<i class="fa fa-check green"></i> {% if prep['num_artifact_children'] > 1 %} <i class="fa fa-check green"></i>{% end%}{% else %}<i class="fa fa-times red"></i>{% end %}, BIOM {% if prep['youngest_artifact_type'] == 'BIOM' %}<i class="fa fa-check green"></i>{% else %}<i class="fa fa-times red"></i>{% end %}
<br />
Created: {{prep['creation_timestamp'].strftime('%B %-d, %Y')}}, last updated: {{prep['modification_timestamp'].strftime('%B %-d, %Y')}}
</a>
</div>
{% end %}
Expand Down