Select the platform (GeneChipId) first

1 files changed, 41 insertions, 8 deletions

diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 09dd3e1..ea47806 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -27,24 +27,57 @@ def make_menu_items_grouper(grouping_fn=lambda item: item):
         return {**acc, grouping: (acc[grouping] + (row_values,))}
     return __grouper__
 
+def species() -> tuple:
+    "Retrieve the species from the database."
+    with database_connection() as conn:
+        with conn.cursor(cursorclass=DictCursor) as cursor:
+            cursor.execute(
+                "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
+                "FROM Species")
+            return tuple(cursor.fetchall())
+
+    return tuple()
+
 def genechips():
     "Retrieve the genechip information from the database"
     def __organise_by_species__(acc, chip):
-        species = chip["species_name"]
-        if acc.get(species) is None:
-            return {**acc, species: (chip,)}
-        return {**acc, species: acc[species] + (chip,)}
+        speciesid = chip["SpeciesId"]
+        if acc.get(speciesid) is None:
+            return {**acc, speciesid: (chip,)}
+        return {**acc, species: acc[speciesid] + (chip,)}
 
     with database_connection() as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
-            cursor.execute(
-                "SELECT GeneChip.*, LOWER(Species.Name) AS species_name "
-                "FROM GeneChip INNER JOIN Species "
-                "ON GeneChip.SpeciesId=Species.SpeciesId")
+            cursor.execute("SELECT * FROM GeneChip ORDER BY GeneChipName ASC")
             return reduce(__organise_by_species__, cursor.fetchall(), {})
 
     return {}
 
+@dbinsertbp.route("/platform", methods=["POST"])
+def select_platform():
+    "Select the platform (GeneChipId) used for the data."
+    job_id = request.form["job_id"]
+    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+        job = jobs.job(rconn, job_id)
+        if job:
+            filename = job["filename"]
+            filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+            if os.path.exists(filepath):
+                default_species = 1
+                gchips = genechips()
+                return render_template(
+                    "select_platform.html", filename=filename,
+                    filetype=job["filetype"], default_species=default_species,
+                    species=species(), genechips=gchips[default_species],
+                    genechips_data=json.dumps(gchips))
+            return render_error(f"File '{filename}' no longer exists.")
+        return render_error(f"Job '{job_id}' no longer exists.")
+    return render_error("Unknown error")
+
+@dbinsertbp.route("/study", methods=["POST"])
+def select_study():
+    return "Not implemented yet"
+
 @dbinsertbp.route("/select-dataset", methods=["POST"])
 def select_dataset():
     "Select the dataset to add the file contents against"