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Add requirements.txt #17

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merged 12 commits into from
Mar 6, 2024
Merged

Add requirements.txt #17

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9ffc2ec
Add requirements.txt
JREastonMarks Mar 1, 2024
9c6df18
Add validate-python yml
JREastonMarks Mar 6, 2024
35958d0
Fix working-directory
JREastonMarks Mar 6, 2024
7838cd9
Another directory change
JREastonMarks Mar 6, 2024
4f75662
test and directory
JREastonMarks Mar 6, 2024
e2f808d
Remove validator
JREastonMarks Mar 6, 2024
0c4de0d
Paths again
JREastonMarks Mar 6, 2024
ec7987f
Formatting
JREastonMarks Mar 6, 2024
dad8eb0
Add docker volume path
JREastonMarks Mar 6, 2024
486ebff
Change dir
JREastonMarks Mar 6, 2024
689b947
More directory fixes
JREastonMarks Mar 6, 2024
ac609af
Update directory report html
JREastonMarks Mar 6, 2024
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26 changes: 26 additions & 0 deletions .github/workflows/validate-python.yml
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name: Python validator

on: [push, pull_request]

jobs:
build:
name: Validate Data
runs-on: ubuntu-latest
steps:
- name: 'Checkout Code'
uses: actions/checkout@v4
with:
path: ./cbioportal-core
- name: 'Validate tests'
working-directory: ./cbioportal-core
run: |
docker run -v ${PWD}:/cbioportal-core python:3.6 /bin/sh -c '
cd cbioportal-core &&
pwd &&
ls -lart &&
pip install -r requirements.txt &&
export PYTHONPATH=/cbioportal-core/src/main/resources/scripts &&
cd src/test/scripts/ &&
python unit_tests_validate_data.py &&
python system_tests_validate_data.py &&
python system_tests_validate_studies.py'
6 changes: 6 additions & 0 deletions requirements.txt
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@@ -0,0 +1,6 @@
requests==2.20.0
markupsafe==2.0.1
Jinja2==2.11.3
mysqlclient==2.1.0
PyYAML==6.0.1
dsnparse==0.1.15
4 changes: 2 additions & 2 deletions src/test/scripts/test_data/study_es_0/result_report.html
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Expand Up @@ -142,15 +142,15 @@ <h4 class="panel-title">General</h4>
<td><span class="glyphicon glyphicon-cog" aria-hidden="true"></span><span class="sr-only">Debug</span></td>
<td>&ndash;</td>
<td>&ndash;</td>
<td>Retrieving chromosome lengths from &#39;/cbioportal/core/src/main/resources/scripts/importer/chromosome_sizes.json&#39;</td>
<td>Retrieving chromosome lengths from &#39;/cbioportal-core/src/main/resources/scripts/importer/chromosome_sizes.json&#39;</td>
<td>&ndash;</td>
<td></td>
</tr>
<tr class="info">
<td><span class="glyphicon glyphicon-cog" aria-hidden="true"></span><span class="sr-only">Debug</span></td>
<td>&ndash;</td>
<td>&ndash;</td>
<td>Retrieving chromosome lengths from &#39;/cbioportal/core/src/main/resources/scripts/importer/chromosome_sizes.json&#39;</td>
<td>Retrieving chromosome lengths from &#39;/cbioportal-core/src/main/resources/scripts/importer/chromosome_sizes.json&#39;</td>
<td>&ndash;</td>
<td></td>
</tr>
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4 changes: 2 additions & 2 deletions src/test/scripts/test_data/study_es_1/result_report.html
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Expand Up @@ -36,7 +36,7 @@
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<![endif]-->
<title>cBioPortal validation report: study in '/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_1'</title>
<title>cBioPortal validation report: study in '/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_1'</title>
</head>

<body>
Expand All @@ -46,7 +46,7 @@
<div class="header">
<div class="jumbotron">
<h1>cBioPortal validation report</h1>
<p>Study directory:<br />/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_1</p>
<p>Study directory:<br />/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_1</p>
<p>For details, please see <a href='https://github.com/cbioportal/cbioportal/blob/master/docs/File-Formats.md'>the documentation on file formats supported by cBioPortal</a></p>
<p>cBioPortal version -- offline instance</p>
</div>
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4 changes: 2 additions & 2 deletions src/test/scripts/test_data/study_es_3/result_report.html
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Expand Up @@ -36,7 +36,7 @@
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<![endif]-->
<title>cBioPortal validation report: study in '/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_3'</title>
<title>cBioPortal validation report: study in '/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_3'</title>
</head>

<body>
Expand All @@ -46,7 +46,7 @@
<div class="header">
<div class="jumbotron">
<h1>cBioPortal validation report</h1>
<p>Study directory:<br />/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_3</p>
<p>Study directory:<br />/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_3</p>
<p>For details, please see <a href='https://github.com/cbioportal/cbioportal/blob/master/docs/File-Formats.md'>the documentation on file formats supported by cBioPortal</a></p>
<p>cBioPortal version unknown -- offline instance</p>
</div>
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4 changes: 2 additions & 2 deletions src/test/scripts/test_data/study_es_3/study_es_3.html
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Expand Up @@ -36,7 +36,7 @@
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<![endif]-->
<title>cBioPortal validation report: study in '/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_3'</title>
<title>cBioPortal validation report: study in '/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_3'</title>
</head>

<body>
Expand All @@ -46,7 +46,7 @@
<div class="header">
<div class="jumbotron">
<h1>cBioPortal validation report</h1>
<p>Study directory:<br />/home/pnp300/git/cbioportal/core/src/test/scripts/test_data/study_es_3</p>
<p>Study directory:<br />/home/pnp300/git/cbioportal-core/src/test/scripts/test_data/study_es_3</p>
<p>For details, please see <a href='https://github.com/cbioportal/cbioportal/blob/master/docs/File-Formats.md'>the documentation on file formats supported by cBioPortal</a></p>
<p>cBioPortal version 1.19.0-SNAPSHOT</p>
</div>
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