From b0991ec5cea1411237b82e92467603bf9da803f5 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 17 Jun 2025 14:18:24 -0500
Subject: Allow users to provide transposed files.

---
 scripts/rqtl2/phenotypes_qc.py                     |  4 ++--
 uploader/phenotypes/views.py                       |  4 ++++
 .../phenotypes/add-phenotypes-raw-files.html       | 22 ++++++++++++++++++++++
 3 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py
index 699c291..5c89ca0 100644
--- a/scripts/rqtl2/phenotypes_qc.py
+++ b/scripts/rqtl2/phenotypes_qc.py
@@ -209,12 +209,12 @@ def qc_phenocovar_file(
                     (f"Record {_lc} in file {filepath.name} has a different "
                      "number of columns than the number of headings"))),)
             _line = dict(zip(_headings, line))
-            if not bool(_line["description"]):
+            if not bool(_line.get("description")):
                 _errs = _errs + (
                     save_error(InvalidValue(filepath.name,
                                             _line[_headings[0]],
                                             "description",
-                                            _line["description"],
+                                            _line.get("description"),
                                             "The description is not provided!")),)
 
             rconn.hset(file_fqkey(fqkey, "metadata", filepath),
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 6bc7471..f4a302a 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -366,6 +366,7 @@ def process_phenotypes_rqtl2_bundle(error_uri):
 def process_phenotypes_individual_files(error_uri):
     """Process the uploaded individual files."""
     form = request.form
+    _transposed = (form.get("file-transposed") or "off") == "on"
     cdata = {
         "sep": form["file-separator"],
         "comment.char": form["file-comment-character"],
@@ -400,6 +401,9 @@ def process_phenotypes_individual_files(error_uri):
                     arcname=filepath.name)
                 cdata[rqtlkey] = cdata.get(rqtlkey, []) + [filepath.name]
 
+            if rqtlkey not in ("phenocovar",):
+                cdata[f"{rqtlkey}_transposed"] = _transposed
+
         zfile.writestr("control_data.json", data=json.dumps(cdata, indent=2))
 
     return bundlepath
diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
index 697c7ad..5c6aaab 100644
--- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html
+++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
@@ -103,6 +103,28 @@
       <a href="#docs-file-na" title="Documentation for no-value fields">
         documentation for more information</a>.</span>
   </div>
+
+  <div class="form-check form-group">
+    <div class="">
+      <input id="chk-file-transposed"
+             name="file-transposed"
+             type="checkbox"
+             class="form-check-input"
+             style="border: solid #8EABF0" />
+      <label for="chk-file-transposed" class="form-check-label">
+        File transposed</label>
+    </div>
+    <span class="form-text text-muted">
+      We expect the data in the file as a matrix of
+      <strong>samples × phenotypes</strong>, but it could be your file is
+      transposed, (i.e. it is a matrix of
+      &ldquo;<em>phenotypes × samples</em>&rdquo;, rather than the expected
+      form).
+      <br />
+      If that is the case for your files, mark your files as trasposed by
+      ensuring that this checkbox is checked.
+    </span>
+  </div>
 </fieldset>
 
 <fieldset id="fldset-data-files">
-- 
cgit 1.4.1