From 0369fc21eaa54466bd64f3b12d1fe6a1dbc81de0 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 18 Jan 2024 13:13:52 +0300
Subject: UI: Select from existing ProbeSet datasets.

---
 .../templates/rqtl2/select-probeset-dataset.html   | 45 +++++++++++++++++++++-
 qc_app/upload/rqtl2.py                             | 44 ++++++++++++++++++---
 2 files changed, 81 insertions(+), 8 deletions(-)

(limited to 'qc_app')

diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
index c0c6401..8b9e5ed 100644
--- a/qc_app/templates/rqtl2/select-probeset-dataset.html
+++ b/qc_app/templates/rqtl2/select-probeset-dataset.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%}
 
@@ -8,10 +8,51 @@
 
 <div class="explainer">
   <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
-    file(s). This data needs to be organised under a dataset..</p>
+    file(s). This data needs to be organised under a dataset.</p>
   <p>This page gives you the ability to do that.</p>
 </div>
 
+{{flash_all_messages()}}
+
+<form method="POST"
+      action="{{url_for('upload.rqtl2.select_probeset_dataset',
+	      species_id=species.SpeciesId, population_id=population.Id)}}"
+      id="frm:select-probeset-dataset">
+  <legend class="heading">Select from existing ProbeSet datasets</legend>
+
+  <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}}" />
+  <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+  <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
+
+  <fieldset>
+    <label for="select:probe-dataset">Dataset</label>
+    <select id="select:probe-dataset"
+	    name="probe-dataset-id"
+	    required="required"
+	    {%if datasets | length == 0%}disabled="disabled"{%endif%}>
+      <option value="">Select a dataset</option>
+      {%for dataset in datasets%}
+      <option value={{dataset.Id}}>
+	{{dataset.Name}}
+	{%if dataset.FullName%}
+	 -- ({{dataset.FullName}})
+	{%endif%}
+      </option>
+      {%endfor%}
+    </select>
+  </fieldset>
+
+  <fieldset>
+    <input type="submit"
+	   value="select dataset"
+	   class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+
 <p style="color: red; font-weight: bold;">Under Construction</p>
 
 {%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 0d80776..fc4e0e8 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -172,7 +172,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
             flash("".join(exc.args), "alert-error alert-rqtl2")
             return this_page_with_errors
 
-def check_errors(conn, *args, **kwargs):
+def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statements]
     """Check for select errors in the forms and return a page to redirect to."""
     species_id = kwargs.get("species_id") or request.form.get("species_id")
     population_id = (kwargs.get("population_id")
@@ -208,14 +208,21 @@ def check_errors(conn, *args, **kwargs):
                                 pgsrc="error"),
                         code=307)
 
+    summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
+                                    species_id=species_id,
+                                    population_id=population_id,
+                                    pgsrc="error"),
+                            code=307)
+
     if ("probe-study-id" in args and
         not bool(request.form.get("probe-study-id"))):
         flash("No probeset study was selected!", "alert-error alert-rqtl2")
-        return redirect(url_for("upload.rqtl2.select_probeset_study",
-                                species_id=species_id,
-                                population_id=population_id,
-                                pgsrc="error"),
-                        code=307)
+        return summary_page
+
+    if ("probe-dataset-id" in args and
+        not bool(request.form.get("probe-dataset-id"))):
+        flash("No probeset dataset was selected!", "alert-error alert-rqtl2")
+        return summary_page
 
     return None
 
@@ -325,6 +332,28 @@ def select_probeset_study(species_id: int, population_id: int):
 
         return summary_page
 
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle/select-probeset-dataset"),
+             methods=["POST"])
+def select_probeset_dataset(species_id: int, population_id: int):
+    """Select or create a probeset dataset."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        error = check_errors(
+            conn, "species", "population", "rqtl2_bundle_file", "geno-dataset",
+            "probe-study-id", "probe-dataset-id")
+        if bool(error):
+            return error
+
+        summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
+                                        species_id=species_id,
+                                        population_id=population_id),
+                                code=307)
+        if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))):
+            flash("Invalid dataset selected!", "alert-error alert-rqtl2")
+            return summary_page
+
+        return summary_page
+
 @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
               "/rqtl2-bundle/create-probeset-study"),
              methods=["POST"])
@@ -409,6 +438,8 @@ def select_dataset_info(species_id: int, population_id: int):
                             conn, species_id, population_id),
                     platforms=platforms_by_species(conn, species_id),
                     tissues=all_tissues(conn))
+            probeset_study = probeset_study_by_id(
+                conn, int(form["probe-study-id"]))
 
             if "pheno" in cdata and not bool(form.get("probe-dataset-id")):
                 return render_template(
@@ -417,6 +448,7 @@ def select_dataset_info(species_id: int, population_id: int):
                     population=population,
                     rqtl2_bundle_file=thefile.name,
                     geno_dataset=geno_dataset,
+                    probe_study=probeset_study,
                     datasets=probeset_datasets_by_study(
                         conn, int(form["probe-study-id"])))
 
-- 
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