From 4285cc10e24d6410206329ba079406e9aa21cc30 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 23 Sep 2024 14:30:15 -0500
Subject: Move R/qtl2 upload code under the populations package.

---
 uploader/templates/rqtl2/rqtl2-qc-job-error.html | 120 -----------------------
 1 file changed, 120 deletions(-)
 delete mode 100644 uploader/templates/rqtl2/rqtl2-qc-job-error.html

(limited to 'uploader/templates/rqtl2/rqtl2-qc-job-error.html')

diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
deleted file mode 100644
index 90e8887..0000000
--- a/uploader/templates/rqtl2/rqtl2-qc-job-error.html
+++ /dev/null
@@ -1,120 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}R/qtl2 bundle: QC Job Error{%endblock%}
-
-{%macro errors_table(tableid, errors)%}
-<table id="{{tableid}}" class="table error-table">
-  <caption>{{caption}}</caption>
-  <thead>
-    <tr>
-      <th>Line</th>
-      <th>Column</th>
-      <th>Value</th>
-      <th>Message</th>
-    </tr>
-  </thead>
-  <tbody>
-    {%for error in errors%}
-    <tr>
-      <td>{{error.line}}</td>
-      <td>{{error.column}}</td>
-      <td>{{error.value}}</td>
-      <td>{{error.message}}</td>
-    </tr>
-    {%else%}
-    <tr>
-      <td colspan="4">No errors to display here.</td>
-    </tr>
-    {%endfor%}
-  </tbody>
-</table>
-{%endmacro%}
-
-{%block contents%}
-<h1 class="heading">R/qtl2 bundle: QC job Error</h1>
-
-<div class="explainer">
-  <p>The R/qtl2 bundle has failed some <emph>Quality Control</emph> checks.</p>
-  <p>We list below some of the errors that need to be fixed before the data can
-    be uploaded onto GeneNetwork.</p>
-</div>
-
-{%if errorsgeneric | length > 0%}
-<h2 class="heading">Generic Errors ({{errorsgeneric | length}})</h3>
-<div class="explainer">
-  We found the following generic errors in your R/qtl2 bundle:
-</div>
-
-<h3>Missing Files</h3>
-<div class="explainer">
-  <p>These files are listed in the bundle's control file, but do not actually
-    exist in the bundle</p>
-</div>
-<table id="tbl-errors-missing-files" class="table error-table">
-  <thead>
-    <tr>
-      <th>Control File Key</th>
-      <th>Bundle File Name</th>
-      <th>Message</th>
-    </tr>
-  </thead>
-  <tbody>
-    {%for error in (errorsgeneric | selectattr("type", "equalto", "MissingFile"))%}
-    <tr>
-      <td>{{error.controlfilekey}}</td>
-      <td>{{error.filename}}</td>
-      <td>{{error.message}}</td>
-    </tr>
-    {%endfor%}
-  </tbody>
-</table>
-
-<h3>Other Generic Errors</h3>
-{{errors_table("tbl-errors-generic", errorsgeneric| selectattr("type", "ne", "MissingFile"))}}
-{%endif%}
-
-{%if errorsgeno | length > 0%}
-<h2 class="heading">Geno Errors ({{errorsgeno | length}})</h3>
-<div class="explainer">
-  We found the following errors in the 'geno' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-geno", errorsgeno[0:50])}}
-{%endif%}
-
-{%if errorspheno | length > 0%}
-<h2 class="heading">Pheno Errors ({{errorspheno | length}})</h3>
-<div class="explainer">
-  We found the following errors in the 'pheno' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-pheno", errorspheno[0:50])}}
-{%endif%}
-
-{%if errorsphenose | length > 0%}
-<h2 class="heading">Phenose Errors ({{errorsphenose | length}})</h3>
-<div class="explainer">
-  We found the following errors in the 'phenose' file in your R/qtl2 bundle:
-</div>
-{{errors_table("tbl-errors-phenose", errorsphenose[0:50])}}
-{%endif%}
-
-{%if errorsphenocovar | length > 0%}
-<h2 class="heading">Phenocovar Errors ({{errorsphenocovar | length}})</h3>
-<div class="explainer">
-  We found the following errors in the 'phenocovar' file in your R/qtl2 bundle:
-</div>
-{{errorsphenocovar}}
-{%endif%}
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-<h4>Log</h4>
-<div class="cli-output">
-  <pre>{{"\n".join(messages)}}</pre>
-</div>
-
-{%endblock%}
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