Add Requirements Txt

cBioPortal · Mar 6, 2024 · 189eda6 · 189eda6
1 parent d3dcd44
commit 189eda6
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Showing 6 changed files with 40 additions and 8 deletions.
diff --git a/.github/workflows/validate-python.yml b/.github/workflows/validate-python.yml
@@ -0,0 +1,26 @@
+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'
diff --git a/requirements.txt b/requirements.txt
@@ -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
diff --git a/src/test/scripts/test_data/study_es_0/result_report.html b/src/test/scripts/test_data/study_es_0/result_report.html
@@ -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>

diff --git a/src/test/scripts/test_data/study_es_1/result_report.html b/src/test/scripts/test_data/study_es_1/result_report.html
@@ -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>
@@ -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>

diff --git a/src/test/scripts/test_data/study_es_3/result_report.html b/src/test/scripts/test_data/study_es_3/result_report.html
@@ -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>
@@ -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>

diff --git a/src/test/scripts/test_data/study_es_3/study_es_3.html b/src/test/scripts/test_data/study_es_3/study_es_3.html
@@ -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>
@@ -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>