From d809997e8ca76d2441b58693078c6c9698e769bb Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 16 Jan 2024 12:38:30 +0300
Subject: Create intermediate step

We do not have the option to modify the request and then redirect with
the modification in place. To go around that, this commit creates an
intermediate step that informs the user of their progress, while
allowing us to store the filename for future steps.
---
 .../rqtl2/upload-rqtl2-bundle-step-01.html         | 44 ++++++++++++++++++++++
 qc_app/templates/rqtl2/upload-rqtl2-bundle.html    | 44 ----------------------
 qc_app/upload/rqtl2.py                             |  8 +++-
 3 files changed, 50 insertions(+), 46 deletions(-)
 create mode 100644 qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
 delete mode 100644 qc_app/templates/rqtl2/upload-rqtl2-bundle.html

diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
new file mode 100644
index 0000000..6491e6b
--- /dev/null
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
@@ -0,0 +1,44 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Upload R/qtl2 Bundle</h2>
+
+<form id="frm-upload-rqtl2-bundle"
+      action="{{url_for('upload.rqtl2.upload_rqtl2_bundle',
+	      species_id=species.SpeciesId,
+	      population_id=population.InbredSetId)}}"
+      method="POST"
+      enctype="multipart/form-data">
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+  <input type="hidden" name="population_id"
+	 value="{{population.InbredSetId}}" />
+
+  {{flash_messages("error-rqtl2")}}
+
+  <fieldset>
+    <legend>file upload</legend>
+    <label for="file:rqtl2-bundle">R/qtl2 bundle</label>
+    <input type="file" id="file:rqtl2-bundle" name="rqtl2_bundle"
+	   accept="application/zip, .zip"
+	   required="required" />
+    <span class="form-input-help"><p>Provide a valid R/qtl2 zip file here. In
+      particular, ensure your zip bundle contains exactly one control file and
+      the corresponding files mentioned in the control file.</p>
+      <p>The control file can be either a YAML or JSON file. <em>ALL</em> other
+	data files in the zip bundle should be CSV files.</p>
+      <p>See the
+	<a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html"
+	   target="_blank">
+	  R/qtl2 file format specifications</a> for more details.</p></span>
+  </fieldset>
+  <fieldset>
+    <input type="submit"
+	   value="upload R/qtl2 bundle"
+	   class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+
+{%endblock%}
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle.html
deleted file mode 100644
index 6491e6b..0000000
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle.html
+++ /dev/null
@@ -1,44 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload R/qtl2 Bundle{%endblock%}
-
-{%block contents%}
-<h2 class="heading">Upload R/qtl2 Bundle</h2>
-
-<form id="frm-upload-rqtl2-bundle"
-      action="{{url_for('upload.rqtl2.upload_rqtl2_bundle',
-	      species_id=species.SpeciesId,
-	      population_id=population.InbredSetId)}}"
-      method="POST"
-      enctype="multipart/form-data">
-  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-  <input type="hidden" name="population_id"
-	 value="{{population.InbredSetId}}" />
-
-  {{flash_messages("error-rqtl2")}}
-
-  <fieldset>
-    <legend>file upload</legend>
-    <label for="file:rqtl2-bundle">R/qtl2 bundle</label>
-    <input type="file" id="file:rqtl2-bundle" name="rqtl2_bundle"
-	   accept="application/zip, .zip"
-	   required="required" />
-    <span class="form-input-help"><p>Provide a valid R/qtl2 zip file here. In
-      particular, ensure your zip bundle contains exactly one control file and
-      the corresponding files mentioned in the control file.</p>
-      <p>The control file can be either a YAML or JSON file. <em>ALL</em> other
-	data files in the zip bundle should be CSV files.</p>
-      <p>See the
-	<a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html"
-	   target="_blank">
-	  R/qtl2 file format specifications</a> for more details.</p></span>
-  </fieldset>
-  <fieldset>
-    <input type="submit"
-	   value="upload R/qtl2 bundle"
-	   class="btn btn-main form-col-2" />
-  </fieldset>
-</form>
-
-{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index d60ea65..0eca6ae 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -132,7 +132,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
         if request.method == "GET" or (
                 request.method == "POST"
                 and bool(request.args.get("pgsrc"))):
-            return render_template("rqtl2/upload-rqtl2-bundle.html",
+            return render_template("rqtl2/upload-rqtl2-bundle-step-01.html",
                                    species=species,
                                    population=population)
 
@@ -150,7 +150,11 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
         try:
             with ZipFile(str(the_file), "r") as zfile:
                 r_qtl2.validate_bundle(zfile)
-                return "WOULD PROCESS THE BUNDLE..."
+                return render_template(
+                    "rqtl2/upload-rqtl2-bundle-step-02.html",
+                    species=species,
+                    population=population,
+                    rqtl2_bundle_file=the_file.name)
         except (InvalidFormat, __RequestError__) as exc:
             flash("".join(exc.args), "alert-error alert-danger error-rqtl2")
             return this_page_with_errors
-- 
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