From 8595c75345fb5849a4d8894f3ee7a926dd8cdf8f Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 8 Jan 2024 07:25:35 +0300
Subject: Upload R/qtl2 zip bundle and check for errors.

---
 qc_app/static/css/styles.css                    |  5 +++
 qc_app/templates/rqtl2/upload-rqtl2-bundle.html | 44 +++++++++++++++++++
 qc_app/upload/rqtl2.py                          | 56 +++++++++++++++++++++++++
 r_qtl/r_qtl2.py                                 | 24 +++++++++++
 4 files changed, 129 insertions(+)
 create mode 100644 qc_app/templates/rqtl2/upload-rqtl2-bundle.html

diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index 8cfd15f..f4112d1 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -156,6 +156,11 @@ fieldset {
     grid-column: 2 / 3;
 }
 
+.form-input-help p {
+    margin-top: 0;
+    margin-bottom: 0.6em;
+}
+
 input[disabled="true"],input[disabled="disabled"] {
     border-color: #878787;
     background-color: #A9A9A9;
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle.html
new file mode 100644
index 0000000..6491e6b
--- /dev/null
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle.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/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 681e54c..53e7f3f 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -1,4 +1,6 @@
 """Module to handle uploading of R/qtl2 bundles."""
+from pathlib import Path
+from zipfile import ZipFile, is_zipfile
 
 from flask import (
     flash,
@@ -9,6 +11,10 @@ from flask import (
     render_template,
     current_app as app)
 
+from r_qtl import r_qtl2
+from r_qtl.errors import InvalidFormat
+
+from qc_app.files import save_file
 from qc_app.dbinsert import species as all_species
 from qc_app.db_utils import with_db_connection, database_connection
 from qc_app.db import (
@@ -96,3 +102,53 @@ def create_population(species_id: int):
                 population_id=new_population["population_id"],
                 pgsrc="create-population"),
         code=307)
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle"),
+    methods=["GET", "POST"])
+def upload_rqtl2_bundle(species_id: int, population_id: int):
+    """Allow upload of R/qtl2 bundle."""
+    this_page_with_errors = redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
+                                             species_id=species_id,
+                                             population_id=population_id,
+                                             pgsrc="error"),
+                                     code=307)
+
+    with database_connection(app.config["SQL_URI"]) as conn:
+        species = species_by_id(conn, species_id)
+        population = population_by_species_and_id(
+            conn, species["SpeciesId"], population_id)
+        if not bool(species):
+            flash("Invalid species!", "alert-error error-rqtl2")
+            return redirect(url_for("upload.rqtl2.select_species"))
+        if not bool(population):
+            flash("Invalid Population!", "alert-error error-rqtl2")
+            return redirect(
+                url_for("upload.rqtl2.select_population", pgsrc="error"),
+                code=307)
+        if request.method == "GET" or (
+                request.method == "POST"
+                and bool(request.args.get("pgsrc"))):
+            return render_template("rqtl2/upload-rqtl2-bundle.html",
+                                   species=species,
+                                   population=population)
+
+        the_file = save_file(
+            request.files.get("rqtl2_bundle"), Path(app.config["UPLOAD_FOLDER"]))
+        if not bool(the_file):
+            flash("Please provide a valid R/qtl2 zip bundle.",
+                  "alert-error alert-danger error-rqtl2")
+            return this_page_with_errors
+
+        if not is_zipfile(the_file):
+            flash("Invalid file! Expected a zip file.",
+                  "alert-error alert-danger error-rqtl2")
+            return this_page_with_errors
+
+        try:
+            with ZipFile(the_file, "r") as zfile:
+                r_qtl2.validate_bundle(zfile)
+                return "WOULD PROCESS THE BUNDLE..."
+        except InvalidFormat as invf:
+            flash("".join(invf.args), "alert-error alert-danger error-rqtl2")
+            return this_page_with_errors
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 2c1e162..a8958a0 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -242,3 +242,27 @@ def sex_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
         yield {
             key: thread_op(value, partial(replace_sex_info, cdata=cdata))
             for key, value in row.items() if key not in ci_fields}
+
+def validate_bundle(zfile: ZipFile):
+    """Ensure the R/qtl2 bundle is valid."""
+    cdata = control_data(zfile)
+    def __member_exists_p__(zfile, member):
+        if isinstance(member, str):
+            zfile.getinfo(member)
+        else:
+            for inner in member:
+                zfile.getinfo(inner)
+
+    try:
+        for member in (key for key in cdata.keys() if key in (
+                "geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap",
+                "pmap")):
+            __member_exists_p__(zfile, cdata[member])
+
+        if "file" in cdata.get("sex", {}):
+            __member_exists_p__(zfile, cdata["sex"]["file"])
+
+        if "file" in cdata.get("cross_info", {}):
+            __member_exists_p__(zfile, cdata["cross_info"]["file"])
+    except KeyError as kerr:
+        raise InvalidFormat(*kerr.args) from kerr
-- 
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