Fetch sample/case names from database

Fetch the sample/case names from the database rather than from a
static file in the repository.

Issue:
https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species

1 files changed, 23 insertions, 2 deletions

diff --git a/qc_app/parse.py b/qc_app/parse.py
index ceb8fcf..40f7b44 100644
--- a/qc_app/parse.py
+++ b/qc_app/parse.py
@@ -7,7 +7,10 @@ from flask import flash, request, url_for, redirect, Blueprint, render_template
 from flask import current_app as app
 
 from quality_control.errors import InvalidValue, DuplicateHeading
-from . import jobs
+
+from qc_app import jobs
+from qc_app.dbinsert import species_by_id
+from qc_app.db_utils import with_db_connection
 
 parsebp = Blueprint("parse", __name__)
 
@@ -23,8 +26,25 @@ def isduplicateheading(item):
 def parse():
     """Trigger file parsing"""
     errors = False
+    speciesid = request.args.get("speciesid")
     filename = request.args.get("filename")
     filetype = request.args.get("filetype")
+    if speciesid is None:
+        flash("No species selected", "alert-error")
+        errors = True
+    else:
+        try:
+            speciesid = int(speciesid)
+            species = with_db_connection(
+                lambda con: species_by_id(con, speciesid))
+            if not bool(species):
+                flash("No such species.", "alert-error")
+                errors = True
+        except ValueError:
+            flash("Invalid speciesid provided. Expected an integer.",
+                  "alert-error")
+            errors = True
+
     if filename is None:
         flash("No file provided", "alert-error")
         errors = True
@@ -50,7 +70,8 @@ def parse():
     with Redis.from_url(redisurl, decode_responses=True) as rconn:
         job = jobs.launch_job(
             jobs.build_file_verification_job(
-                rconn, filepath, filetype, redisurl,
+                rconn, app.config["SQL_URI"], redisurl,
+                speciesid, filepath, filetype,
                 app.config["JOBS_TTL_SECONDS"]),
             redisurl,
             f"{app.config['UPLOAD_FOLDER']}/job_errors")