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Fix Jinja2 undefined variables #417

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merged 1 commit into from
Apr 9, 2024
Merged

Fix Jinja2 undefined variables #417

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2 changes: 1 addition & 1 deletion .github/workflows/integration_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ name: Run Integration Tests

on:
push:

pull_request:
types: [opened, reopened]

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17 changes: 11 additions & 6 deletions CRISPResso2/CRISPRessoReports/CRISPRessoReport.py
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Expand Up @@ -5,22 +5,27 @@
'''

import os
from jinja2 import Environment, FileSystemLoader, PackageLoader, ChoiceLoader
from jinja2 import Environment, FileSystemLoader, ChoiceLoader
from jinja_partials import generate_render_partial, render_partial
from CRISPResso2 import CRISPRessoShared

if CRISPRessoShared.is_C2Pro_installed():
from CRISPRessoPro import __version__ as CRISPRessoProVersion
import CRISPRessoPro
C2PRO_INSTALLED = True
else:
C2PRO_INSTALLED = False


def get_jinja_loader(_ROOT):
if CRISPRessoShared.is_C2Pro_installed():
return Environment(loader=ChoiceLoader([FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')), PackageLoader('CRISPRessoPro', 'templates')]))
def get_jinja_loader(root):
if C2PRO_INSTALLED:
return Environment(
loader=ChoiceLoader([
FileSystemLoader(os.path.join(root, 'CRISPRessoReports', 'templates')),
FileSystemLoader(os.path.join(os.path.dirname(CRISPRessoPro.__file__), 'templates')),
]),
)
else:
return Environment(loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')))
return Environment(loader=FileSystemLoader(os.path.join(root, 'CRISPRessoReports', 'templates')))


def render_template(template_name, jinja2_env, **data):
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8 changes: 2 additions & 6 deletions CRISPResso2/CRISPRessoReports/templates/report.html
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Expand Up @@ -179,7 +179,7 @@ <h5>Global splicing analysis</h5>
{# end of global coding sequence analysis #}

{# start hdr summary #}
{% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] or 'plot_4g' in report_data['figures']['htmls'][amplicon_name] %}
{% if report_data['figures']['locs'][report_data.amplicons[0]]['plot_4g'] or 'plot_4g' in report_data['figures']['htmls'][report_data.amplicons[0]] %}
<div class='card text-center mb-2 breakinpage'>
<div class='card-header'>
{% if report_data.amplicons|length == 1 %} {# if only one amplicon #}
Expand All @@ -189,11 +189,7 @@ <h5>HDR summary report (all reads aligned to {{report_data.amplicons[0]}})</h5>
{% endif %}
</div>
<div class='card-body'>
{% if 'plot_4g' in report_data['figures']['htmls'][amplicon_name] %}
{{ report_data['figures']['htmls'][amplicon_name]['plot_4g']|safe }}
{% else %}
{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', amplicon_name=report_data.amplicons[0])}}
{% endif %}
{{ render_partial('shared/partials/fig_reports.html', report_data=report_data, fig_name='plot_4g', amplicon_name=report_data.amplicons[0])}}
</div>
</div>
{% endif %}
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