From ab71b34b97f3f1eee52b5688f41644541535f281 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 5 Feb 2024 07:00:01 +0300
Subject: Do general bundle validation and show errors

* Display any and all errors on the UI
* Move `validate_bundle` to QC module and refactor to use
  `missing_files`
---
 qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html |  6 +++---
 qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html |  3 ++-
 qc_app/upload/rqtl2.py                                  | 10 ++++++----
 3 files changed, 11 insertions(+), 8 deletions(-)

(limited to 'qc_app')

diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
index 6491e6b..64fcdcd 100644
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-01.html
@@ -1,5 +1,5 @@
 {%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
+{%from "flash_messages.html" import flash_all_messages%}
 
 {%block title%}Upload R/qtl2 Bundle{%endblock%}
 
@@ -16,12 +16,12 @@
   <input type="hidden" name="population_id"
 	 value="{{population.InbredSetId}}" />
 
-  {{flash_messages("error-rqtl2")}}
+  {{flash_all_messages()}}
 
   <fieldset>
     <legend>file upload</legend>
     <label for="file:rqtl2-bundle">R/qtl2 bundle</label>
-    <input type="file" id="file:rqtl2-bundle" name="rqtl2_bundle"
+    <input type="file" id="file:rqtl2-bundle" name="rqtl2_bundle_file"
 	   accept="application/zip, .zip"
 	   required="required" />
     <span class="form-input-help"><p>Provide a valid R/qtl2 zip file here. In
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
index 9269a3c..01721e9 100644
--- a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
@@ -1,5 +1,5 @@
 {%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
+{%from "flash_messages.html" import flash_all_messages%}
 
 {%block title%}Upload R/qtl2 Bundle{%endblock%}
 
@@ -20,6 +20,7 @@
 	      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}}" />
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index eea49e1..2d032f8 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -18,6 +18,8 @@ from flask import (
     current_app as app)
 
 from r_qtl import r_qtl2
+from r_qtl import errors as rqe
+from r_qtl import r_qtl2_qc as rqc
 from r_qtl.errors import InvalidFormat
 
 from qc_app import jobs
@@ -157,11 +159,11 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
                                    species=species,
                                    population=population)
 
-        if not bool(request.files.get("rqtl2_bundle")):
+        if not bool(request.files.get("rqtl2_bundle_file")):
             raise __RequestError__("No R/qtl2 zip bundle provided.")
 
-        the_file = save_file(
-            request.files["rqtl2_bundle"], Path(app.config["UPLOAD_FOLDER"]))
+        the_file = save_file(request.files["rqtl2_bundle_file"],
+                             Path(app.config["UPLOAD_FOLDER"]))
         if not bool(the_file):
             raise __RequestError__("Please provide a valid R/qtl2 zip bundle.")
 
@@ -170,7 +172,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
 
         try:
             with ZipFile(str(the_file), "r") as zfile:
-                r_qtl2.validate_bundle(zfile)
+                rqc.validate_bundle(zfile)
                 return render_template(
                     "rqtl2/upload-rqtl2-bundle-step-02.html",
                     species=species,
-- 
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