Rename module: qc_app --> uploader

1 files changed, 120 insertions, 0 deletions

diff --git a/uploader/templates/rqtl2/rqtl2-qc-job-error.html b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
new file mode 100644
index 0000000..90e8887
--- /dev/null
+++ b/uploader/templates/rqtl2/rqtl2-qc-job-error.html
@@ -0,0 +1,120 @@
+{%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%}