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Fix validation of long format
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Bas Leenknegt committed Nov 16, 2022
1 parent 11d7217 commit 773bff4
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Showing 5 changed files with 61 additions and 115 deletions.
2 changes: 1 addition & 1 deletion core/src/test/scripts/system_tests_validate_studies.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ def test_exit_status_success_for_legacy_cna_discrete(self):
"""

# Build up arguments and run
print("===study 0")
print("===study 0 legacy")
args = ['--list-of-studies', 'test_data/study_es_0_legacy_cna_discrete/',
'--portal_info_dir', PORTAL_INFO_DIR]
args = validateStudies.interface(args)
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1 change: 0 additions & 1 deletion core/src/test/scripts/test_data/study_es_0/meta_cna_discrete.txt
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Expand Up @@ -6,4 +6,3 @@ show_profile_in_analysis_tab: true
profile_description: Putative copy-number from GISTIC 2.0. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification.
profile_name: Putative copy-number alterations from GISTIC
data_filename: data_cna_discrete.txt
namespaces: CustomNamespace
167 changes: 55 additions & 112 deletions core/src/test/scripts/test_data/study_es_0/result_report.html
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Expand Up @@ -616,7 +616,7 @@ <h4 class="panel-title">data_clinical_samples.txt</h4>
<a role="button" data-toggle="collapse" aria-expanded="true"
href="#collapse_ZGF0YV9jbmFfZGlzY3JldGUudHh0",
aria-controls="collapse_ZGF0YV9jbmFfZGlzY3JldGUudHh0">
<span class="badge">3</span>
<span class="badge">4</span>
<h4 class="panel-title">data_cna_discrete.txt</h4>
</a>
</div>
Expand Down Expand Up @@ -644,6 +644,59 @@ <h4 class="panel-title">data_cna_discrete.txt</h4>
<td>&ndash;</td>
<td></td>
</tr>
<tr class="success">
<td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
<td>154, 155, 844&hellip;</td>
<td>6</td>
<td>Values contained in the column cbp_driver_tiers that will appear in the &#34;Mutation Color&#34; menu of the Oncoprint</td>
<td>Class 2, Class 1</td>
<td><!-- Trigger/Open The Modal -->
<a href="#showValues" data-toggle="modal" data-backdrop="false" data-target=".modaldata_cna_discrete2value">See all 4 values </a>

<div class="modal fade modaldata_cna_discrete2value" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
<h4 class="modal-title" id="gridSystemModalLabel">Listing all values for the message: Values contained in the column cbp_driver_tiers that will appear in the &#34;Mutation Color&#34; menu of the Oncoprint</h4>
</div>
<div class="modal-body">
<table class="table">
<thead>
<tr>
<th>Line Number</th>
<th>Column Number</th>
<th>Value Encountered</th>
</tr>
</thead>
<tbody>
<tr>
<td>154</td>
<td>6</td>
<td>Class 2</td>
</tr>
<tr>
<td>155</td>
<td>6</td>
<td>Class 1</td>
</tr>
<tr>
<td>844</td>
<td>6</td>
<td>Class 2</td>
</tr>
<tr>
<td>845</td>
<td>6</td>
<td>Class 1</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div></td>
</tr>
<tr class="success">
<td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
<td>&ndash;</td>
Expand All @@ -656,7 +709,7 @@ <h4 class="panel-title">data_cna_discrete.txt</h4>
<td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
<td>&ndash;</td>
<td>&ndash;</td>
<td>Read 9 lines. Lines with warning: 0. Lines with error: 0</td>
<td>Read 6305 lines. Lines with warning: 0. Lines with error: 0</td>
<td>&ndash;</td>
<td></td>
</tr>
Expand Down Expand Up @@ -780,116 +833,6 @@ <h4 class="panel-title">data_cna_log2.txt</h4>
</div>
</div>

<div class="panel panel-success">
<div class="panel-heading" role="tab"
id="heading_ZGF0YV9jbmFfcGRfYW5ub3RhdGlvbnMudHh0">
<span class="header-icon"><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></span>
<a role="button" data-toggle="collapse" aria-expanded="true"
href="#collapse_ZGF0YV9jbmFfcGRfYW5ub3RhdGlvbnMudHh0",
aria-controls="collapse_ZGF0YV9jbmFfcGRfYW5ub3RhdGlvbnMudHh0">
<span class="badge">4</span>
<h4 class="panel-title">data_cna_pd_annotations.txt</h4>
</a>
</div>
<div class="panel-collapse collapse" role="tabpanel"
id="collapse_ZGF0YV9jbmFfcGRfYW5ub3RhdGlvbnMudHh0"
aria-labelledby="heading_ZGF0YV9jbmFfcGRfYW5ub3RhdGlvbnMudHh0">
<div class="panel-body">
<table class="table">
<thead>
<tr>
<th></th>
<th>Line Number</th>
<th>Column Number</th>
<th>Message</th>
<th>Value Encountered</th>
<th></th>
</tr>
</thead>
<tbody>
<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>Starting validation of file</td>
<td>&ndash;</td>
<td></td>
</tr>
<tr class="success">
<td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
<td>2, 3, 6&hellip;</td>
<td>4</td>
<td>Values contained in the column cbp_driver_tiers that will appear in the &#34;Mutation Color&#34; menu of the Oncoprint</td>
<td>Class 2, Class 1</td>
<td><!-- Trigger/Open The Modal -->
<a href="#showValues" data-toggle="modal" data-backdrop="false" data-target=".modaldata_cna_pd_annotations2value">See all 4 values </a>

<div class="modal fade modaldata_cna_pd_annotations2value" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
<h4 class="modal-title" id="gridSystemModalLabel">Listing all values for the message: Values contained in the column cbp_driver_tiers that will appear in the &#34;Mutation Color&#34; menu of the Oncoprint</h4>
</div>
<div class="modal-body">
<table class="table">
<thead>
<tr>
<th>Line Number</th>
<th>Column Number</th>
<th>Value Encountered</th>
</tr>
</thead>
<tbody>
<tr>
<td>2</td>
<td>4</td>
<td>Class 2</td>
</tr>
<tr>
<td>3</td>
<td>4</td>
<td>Class 1</td>
</tr>
<tr>
<td>6</td>
<td>4</td>
<td>Class 2</td>
</tr>
<tr>
<td>7</td>
<td>4</td>
<td>Class 1</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div></td>
</tr>
<tr class="success">
<td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
<td>&ndash;</td>
<td>&ndash;</td>
<td>Validation of file complete</td>
<td>&ndash;</td>
<td></td>
</tr>
<tr class="success">
<td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
<td>&ndash;</td>
<td>&ndash;</td>
<td>Read 8 lines. Lines with warning: 0. Lines with error: 0</td>
<td>&ndash;</td>
<td></td>
</tr>
</tbody>
</table>
</div>
</div>
</div>

<div class="panel panel-success">
<div class="panel-heading" role="tab"
id="heading_ZGF0YV9leHByZXNzaW9uX21lZGlhbi50eHQ">
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