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Merge pull request #290 from biocore/csymons_production_feedback
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Addressing Feedback from Production Testing
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@cassidysymons
cassidysymons authored Sep 13, 2023
2 parents 094a148 + 6a988f3 commit 58ffead
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Showing 16 changed files with 729 additions and 444 deletions.
96 changes: 72 additions & 24 deletions microsetta_interface/implementation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from datetime import datetime
import base64
import functools
import re
from string import ascii_lowercase
from microsetta_interface.model_i18n import translate_source, \
translate_sample, translate_survey_template, EN_US_KEY, LANGUAGES, \
Expand Down Expand Up @@ -389,6 +390,8 @@ class Source:
OTHER_ID
]

DAKLAPACK_KIT_RE = re.compile(r"DMK[234689ACDEFHJKMNPRTVWXY]{6}")


def _render_with_defaults(template_name, **context):
defaults = {}
Expand Down Expand Up @@ -1092,14 +1095,18 @@ def get_account(*, account_id=None):

# Determine if the source/profile has any action items. This framework
# will evolve over time.
non_human_sources = False
for s in sources:
alerts = 0
if s['source_type'] == Source.SOURCE_TYPE_HUMAN:

need_reconsent_d = check_current_consent(
account_id, s[SOURCE_ID], "data"
)
if need_reconsent_d:
alerts += 1
need_reconsent_d = check_current_consent(
account_id, s[SOURCE_ID], "data"
)
if need_reconsent_d:
alerts += 1
else:
non_human_sources = True

s['alerts'] = alerts

Expand All @@ -1113,7 +1120,8 @@ def get_account(*, account_id=None):
return _render_with_defaults('account_overview.jinja2',
account=account,
sources=sources,
japan_user=japan_user)
japan_user=japan_user,
non_human_sources=non_human_sources)


@prerequisite([ACCT_PREREQS_MET])
Expand Down Expand Up @@ -1396,11 +1404,6 @@ def get_fill_source_survey(*,
ctr = 0
trig_ctr = 0
for field in group['fields']:
if need_reconsent:
# If the user has not agreed to the current consent, we
# disable all of the fields.
field['disabled'] = True

if "triggered_by" in field:
field['label'] = str(ctr) + ascii_lowercase[trig_ctr]\
+ ". " + field['label']
Expand All @@ -1410,10 +1413,22 @@ def get_fill_source_survey(*,
ctr += 1
survey_question_count += 1
field['label'] = str(ctr) + ". " + field['label']
field['label'] = '<span class="survey-skip small-text" '\
+ 'onClick="skipQuestion(this)">'\
+ gettext('SKIP')\
+ '</span>' + field['label']

if need_reconsent:
# If the user has not agreed to the current consent, we
# disable all of the fields.
field['disabled'] = True
# And we remove the onClick action from the Skip/Display
# text, but leave it to reflect their last response
field['label'] = '<span ' \
+ 'class="survey-skip-dis small-text">' \
+ gettext('SKIP') \
+ '</span>' + field['label']
else:
field['label'] = '<span class="survey-skip small-text" '\
+ 'onClick="skipQuestion(this)">'\
+ gettext('SKIP')\
+ '</span>' + field['label']

return _render_with_defaults(
"survey.jinja2",
Expand Down Expand Up @@ -1481,14 +1496,16 @@ def get_fill_vioscreen_remote_sample_survey(*,
account_id=None,
source_id=None,
sample_id=None,
registration_code=None):
registration_code=None,
vio_id=None):
suffix = "vspassthru"
redirect_url = SERVER_CONFIG["endpoint"] + \
_make_source_path(account_id, source_id, suffix=suffix)
params = {
'survey_redirect_url': redirect_url,
'vioscreen_ext_sample_id': sample_id,
'registration_code': registration_code
'registration_code': registration_code,
'vio_id': vio_id
}
has_error, survey_output, _ = ApiRequest.get(
'/accounts/%s/sources/%s/survey_templates/%s' %
Expand Down Expand Up @@ -1721,7 +1738,8 @@ def get_source(*, account_id=None, source_id=None):
if survey['survey_template_type'] == "local":
local_surveys.append(survey)
else:
if survey['survey_template_id'] != VIOSCREEN_ID:
if survey['survey_template_id'] != VIOSCREEN_ID and\
survey['survey_template_id'] != POLYPHENOL_FFQ_ID:
if survey['survey_template_id'] == SPAIN_FFQ_ID and\
spain_user is False:
continue
Expand Down Expand Up @@ -1832,17 +1850,23 @@ def get_kits(*, account_id=None, source_id=None, check_survey_date=False):
for sample in samples_output:
if sample['sample_datetime'] is not None:
dt = datetime.fromisoformat(sample['sample_datetime'])
sample['ts_for_sort'] = dt
# rebase=True - show in user's locale, rebase=False, UTC (I think?)
sample['sample_datetime'] = flask_babel.format_datetime(
dt,
format=None, # Use babel default (short/medium/long/full)
rebase=False)
else:
# We just need a sort value for samples without a collection date
# and we want it to filter to the top when we sort by date desc.
sample['ts_for_sort'] = datetime.fromisoformat("9999-12-31")

is_human = source_output['source_type'] == Source.SOURCE_TYPE_HUMAN

samples = [translate_sample(s) for s in samples_output]

kits = defaultdict(list)
kits_ts = {}
for s in samples:
if s['sample_site'] == '' or s['sample_datetime'] == '':
s['css_class'] = "sample-needs-info"
Expand All @@ -1852,6 +1876,18 @@ def get_kits(*, account_id=None, source_id=None, check_survey_date=False):
s['alert_icon'] = "green_checkmark.svg"

kits[s['kit_id']].append(s)
if s['kit_id'] in kits_ts:
if s['ts_for_sort'] > kits_ts[s['kit_id']]:
kits_ts[s['kit_id']] = s['ts_for_sort']
else:
kits_ts[s['kit_id']] = s['ts_for_sort']

sorted_kits = {}
sorted_kits_ts = dict(
sorted(kits_ts.items(), key=lambda x: x[1], reverse=True)
)
for kit_id in sorted_kits_ts.keys():
sorted_kits[kit_id] = kits[kit_id]

profile_has_samples = _check_if_source_has_samples(account_id, source_id)

Expand Down Expand Up @@ -1879,7 +1915,7 @@ def get_kits(*, account_id=None, source_id=None, check_survey_date=False):
account_id=account_id,
source_id=source_id,
is_human=is_human,
kits=kits,
kits=sorted_kits,
source_name=source_output['source_name'],
fundrazr_url=SERVER_CONFIG["fundrazr_url"],
account_country=account_country,
Expand Down Expand Up @@ -1928,6 +1964,9 @@ def get_nutrition(*, account_id=None, source_id=None, new_ffq_code=None):
return vioscreen_output

profile_has_samples = _check_if_source_has_samples(account_id, source_id)
need_reconsent_data = check_current_consent(
account_id, source_id, "data"
)

return _render_with_defaults(
'nutrition.jinja2',
Expand All @@ -1940,7 +1979,8 @@ def get_nutrition(*, account_id=None, source_id=None, new_ffq_code=None):
nutrition_tab_whitelist=NUTRITION_TAB_WHITELIST,
new_ffq_code=new_ffq_code,
profile_has_samples=profile_has_samples,
has_basic_info=has_basic_info
has_basic_info=has_basic_info,
need_reconsent_data=need_reconsent_data
)


Expand Down Expand Up @@ -2011,9 +2051,7 @@ def get_consents(*, account_id=None, source_id=None):
)
if has_error:
if has_error == 404:
# If historical users who haven't re-consented try to view signed
# consents, we redirect them to the consent page
return render_consent_page(account_id, source_id, "data")
data_consent = None
else:
return data_consent

Expand Down Expand Up @@ -2074,14 +2112,20 @@ def get_consent_view(*, account_id=None, source_id=None, consent_type=None):
False
)

if consent_type == "biospecimen":
consent_type_display = "Biospecimen"
else:
consent_type_display = "Survey"

return _render_with_defaults(
'signed_consent.jinja2',
account_id=account_id,
source_id=source_id,
source_age=source_output['consent']['age_range'],
source_name=source_output['source_name'],
consent=consent_output,
tl=consent_assets
tl=consent_assets,
consent_type_display=consent_type_display
)


Expand Down Expand Up @@ -2480,12 +2524,16 @@ def admin_barcode_search_query_qiita(body):


def get_ajax_check_kit_valid(kit_name):
if DAKLAPACK_KIT_RE.match(kit_name.upper()):
kit_name = kit_name.upper()
kit, error, _ = _get_kit(kit_name)
result = True if error is None else error
return flask.jsonify(result)


def get_ajax_list_kit_samples(kit_name):
if DAKLAPACK_KIT_RE.match(kit_name.upper()):
kit_name = kit_name.upper()
kit, error, code = _get_kit(kit_name)
result = kit if error is None else error
return flask.jsonify(result), code
Expand Down
5 changes: 5 additions & 0 deletions microsetta_interface/routes.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -792,6 +792,11 @@ paths:
schema:
type: string
nullable: true
- in: query
name: vio_id
schema:
type: string
nullable: true
responses:
'200':
description: Take the vioscreen remote survey
Expand Down
25 changes: 22 additions & 3 deletions microsetta_interface/static/css/minimal_interface.css
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Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,11 @@ h2.account-h2 {

h2.profile-card-h2 {
color: var(--tmi-blue);
height: 40px;
white-space: nowrap;
overflow: hidden;
text-overflow: ellipsis;
max-width: 90%;
}

h3 {
Expand Down Expand Up @@ -458,7 +463,7 @@ p.tmi-content {

@media (max-width: 575.98px) {
.card-survey {
height: 230px;
height: 280px;
}

.card-survey-external {
Expand Down Expand Up @@ -683,8 +688,8 @@ h1.profile-h1 {
color: var(--tmi-gray-80);
}

@media (max-width: 575.98px) {
.survey-info-row {
@media (max-width: 359.98px) {
.survey-info-row > .text-end {
display: none;
}
}
Expand Down Expand Up @@ -894,6 +899,16 @@ li.active-profile {
text-decoration: underline;
}

.survey-skip-dis {
float: right;
margin-right: 10px;
color: var(--tmi-gray-80) !important;
font-weight: 400 !important;
font-size: 12px !important;
line-height: 20px !important;
text-decoration: none;
}

.skip-text {
color: var(--tmi-gray-80) !important;
font-weight: 400 !important;
Expand Down Expand Up @@ -1267,6 +1282,10 @@ input.barcode-checkbox[type=checkbox]:checked+label {
margin-left: auto;
}

.barcode-col > .btn {
display: inline;
}

.barcode-text {
color: var(--tmi-blue);
font-weight: 700;
Expand Down
30 changes: 29 additions & 1 deletion microsetta_interface/templates/account_overview.jinja2
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,9 @@
<div class="container default-container">
{% if sources|length > 0 %}
<h2 class="account-h2">{{ _('Active Profiles') }}</h2>
{% if non_human_sources %}
<p class="tmi-tooltip">{{ _('Please note: animal and environmental profiles are currently unavailable.') }}</p>
{% endif %}
<div class="row mb-5">
{% for source in sources %}
<div class="col-md-4 mb-4">
Expand All @@ -66,13 +69,31 @@
</div>
</div>
{% else %}
{% if source.source_type == "animal" %}
<div class="card card-profile">
<img src="/static/img/source_animal.png" class="mx-auto card-profile-icon" width="70px">
<h2 class="profile-card-h2 mx-auto mt-2 mb-4" title="{{ source.source_name|e}}">{{ source.source_name|e}}</h2>
<a class="btn btn-blue-gradient mx-auto" style="width: fit-content; pointer-events: none;" href="#" disabled>
{{ _('Unavailable') }}
</a>
</div>
{% elif source.source_type == "environmental" %}
<div class="card card-profile">
<img src="/static/img/source_environmental.png" class="mx-auto card-profile-icon" width="70px">
<h2 class="profile-card-h2 mx-auto mt-2 mb-4" title="{{ source.source_name|e}}">{{ source.source_name|e}}</h2>
<a class="btn btn-blue-gradient mx-auto" style="width: fit-content; pointer-events: none;" href="#" disabled>
{{ _('Unavailable') }}
</a>
</div>
{% else %}
<div class="card card-profile">
<img src="/static/img/profile_card_icon.png" class="mx-auto card-profile-icon">
<h2 class="profile-card-h2 mx-auto mt-2 mb-4">{{ source.source_name|e}}</h2>
<h2 class="profile-card-h2 mx-auto mt-2 mb-4" title="{{ source.source_name|e}}">{{ source.source_name|e}}</h2>
<a class="btn btn-blue-gradient mx-auto" style="width: fit-content;" href="/accounts/{{account.account_id}}/sources/{{ source.source_id|e }}">
{{ _('Go to My Profile') }}
</a>
</div>
{% endif %}
{% endif %}
</div>
{% endfor %}
Expand Down Expand Up @@ -106,6 +127,13 @@
<p class="disabled-source-types"><strong>{{ _('Coming Soon') }}</strong></p>
</div>
</div>
{% if admin_mode %}
<div class="row mt-3">
<div class="col-12">
<center><h2><a href="/accounts/{{ account.account_id }}/details">{{ _('Account Details') }}</a></h2></center>
</div>
</div>
{% endif %}
</div>


Expand Down
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