From d02cef83c3c0b3f3098df1a7e7eeaf90430f784a Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 8 Feb 2024 15:54:32 +0300
Subject: R/qtl2 QC: Set up scaffolding for QC UI

Set up the scaffolding for the flows and UI that will be used when
running QC against the uploaded R/qtl2 bundle.

This will be fleshed out later, and the UI is likely to change
somewhat, down the line.
---
 qc_app/templates/base.html                       |  2 +-
 qc_app/templates/rqtl2/rqtl2-qc-job-error.html   | 32 ++++++++++++++++++++
 qc_app/templates/rqtl2/rqtl2-qc-job-status.html  | 29 +++++++++++++++++++
 qc_app/templates/rqtl2/rqtl2-qc-job-success.html | 37 ++++++++++++++++++++++++
 4 files changed, 99 insertions(+), 1 deletion(-)
 create mode 100644 qc_app/templates/rqtl2/rqtl2-qc-job-error.html
 create mode 100644 qc_app/templates/rqtl2/rqtl2-qc-job-status.html
 create mode 100644 qc_app/templates/rqtl2/rqtl2-qc-job-success.html

(limited to 'qc_app/templates')

diff --git a/qc_app/templates/base.html b/qc_app/templates/base.html
index 3b701bc..2228356 100644
--- a/qc_app/templates/base.html
+++ b/qc_app/templates/base.html
@@ -6,7 +6,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     {%block extrameta%}{%endblock%}
 
-    <title>QC: {%block title%}{%endblock%}</title>
+    <title>GN Uploader: {%block title%}{%endblock%}</title>
 
     <link rel="stylesheet" type="text/css" href="/static/css/styles.css" />
     {%block css%}{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-error.html b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
new file mode 100644
index 0000000..5d2ebee
--- /dev/null
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-error.html
@@ -0,0 +1,32 @@
+{%extends "base.html"%}
+{%from "cli-output.html" import cli_output%}
+
+{%block title%}R/qtl2 bundle: QC Job Error{%endblock%}
+
+{%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>
+
+<h2 class="heading">Errors</h2>
+
+<p><emph>list errors here by file type, I think &hellip;</emph></p>
+
+<h4>stdout</h4>
+{{cli_output(job, "stdout")}}
+
+<h4>stderr</h4>
+{{cli_output(job, "stderr")}}
+
+<h4>Log</h4>
+<div class="cli-output">
+  {%for msg in messages%}
+  {{msg}}<br />
+  {%endfor%}
+</div>
+
+{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-status.html b/qc_app/templates/rqtl2/rqtl2-qc-job-status.html
new file mode 100644
index 0000000..85b8864
--- /dev/null
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-status.html
@@ -0,0 +1,29 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Job Status{%endblock%}
+
+{%block extrameta%}
+<meta http-equiv="refresh" content="3">
+{%endblock%}
+
+{%block contents%}
+<h1 class="heading">R/qtl2 bundle: QC job status</h1>
+
+<h2 class="heading">R/qtl2 bundle: QC Job Status</h2>
+
+<hr />
+<p>The job:</p>
+<hr />
+{{job}}
+<hr />
+<hr />
+
+<h4>Log</h4>
+<div class="cli-output">
+  {%for msg in messages%}
+  {{msg}}<br />
+  {%endfor%}
+</div>
+
+{%endblock%}
diff --git a/qc_app/templates/rqtl2/rqtl2-qc-job-success.html b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
new file mode 100644
index 0000000..396f241
--- /dev/null
+++ b/qc_app/templates/rqtl2/rqtl2-qc-job-success.html
@@ -0,0 +1,37 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}R/qtl2 Bundle: Quality Control Successful{%endblock%}
+
+{%block contents%}
+<h2 class="heading">R/qtl2 Bundle: Quality Control Successful</h2>
+
+<div class="explainer">
+  <p>The R/qtl2 bundle you uploaded has passed <emph>all</emph> quality control
+    checks successfully, and is now ready for uploading into the database.</p>
+  <p>Click "Continue" below to proceed.</p>
+</div>
+
+<!--
+    The "action" on this form takes us to the next step, where we can
+    select all the other data necessary to enter the data into the database.
+  -->
+<form id="frm-upload-rqtl2-bundle"
+      action="{{url_for('upload.rqtl2.select_dataset_info',
+	      species_id=species.SpeciesId,
+	      population_id=population.InbredSetId)}}"
+      method="POST"
+      enctype="multipart/form-data">
+  {{flash_all_messages()}}
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+  <input type="hidden" name="population_id"
+	 value="{{population.InbredSetId}}" />
+  <input type="hidden" name="rqtl2_bundle_file"
+	 value="{{rqtl2_bundle_file}}" />
+
+  <fieldset>
+    <input type="submit" value="continue" class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+
+{%endblock%}
-- 
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