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-rw-r--r--qc_app/default_settings.py2
-rw-r--r--tests/conftest.py2
-rw-r--r--tests/test_instance_dir/config.py2
-rw-r--r--tests/uploader/test_parse.py2
-rw-r--r--uploader/expression_data/dbinsert.py6
-rw-r--r--uploader/expression_data/views.py10
-rw-r--r--uploader/flask_extensions.py6
-rw-r--r--uploader/oauth2/client.py15
-rw-r--r--uploader/population/rqtl2.py6
-rw-r--r--uploader/samples/views.py27
10 files changed, 51 insertions, 27 deletions
diff --git a/qc_app/default_settings.py b/qc_app/default_settings.py
index 7a9da0f..7bb0bf8 100644
--- a/qc_app/default_settings.py
+++ b/qc_app/default_settings.py
@@ -7,7 +7,7 @@ import os
 
 LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING")
 SECRET_KEY = b"<Please! Please! Please! Change This!>"
-UPLOAD_FOLDER = "/tmp/qc_app_files"
+UPLOADS_DIRECTORY = "/tmp/qc_app_files"
 REDIS_URL = "redis://"
 JOBS_TTL_SECONDS = 1209600 # 14 days
 GNQC_REDIS_PREFIX="GNQC"
diff --git a/tests/conftest.py b/tests/conftest.py
index a716c52..2009aab 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -183,7 +183,7 @@ def redis_conn_with_completed_job_some_errors(redis_url, redis_ttl, jobs_prefix,
 def uploads_dir(client): # pylint: disable=[redefined-outer-name]
     """Returns the configured, uploads directory, creating it if it does not
     exist."""
-    the_dir = client.application.config["UPLOAD_FOLDER"]
+    the_dir = client.application.config["UPLOADS_DIRECTORY"]
     if not os.path.exists(the_dir):
         os.mkdir(the_dir)
 
diff --git a/tests/test_instance_dir/config.py b/tests/test_instance_dir/config.py
index 2ee569b..f04b3df 100644
--- a/tests/test_instance_dir/config.py
+++ b/tests/test_instance_dir/config.py
@@ -6,6 +6,6 @@ import os
 
 LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING")
 SECRET_KEY = b"<Please! Please! Please! Change This!>"
-UPLOAD_FOLDER = "/tmp/qc_app_files"
+UPLOADS_DIRECTORY = "/tmp/qc_app_files"
 REDIS_URL = "redis://"
 JOBS_TTL_SECONDS = 600 # 10 minutes
diff --git a/tests/uploader/test_parse.py b/tests/uploader/test_parse.py
index 20c75b7..56e1b41 100644
--- a/tests/uploader/test_parse.py
+++ b/tests/uploader/test_parse.py
@@ -50,7 +50,7 @@ def test_parse_with_existing_uploaded_file(
     assert the_job["command"] == " ".join([
         sys.executable, "-m", "scripts.validate_file", db_url, redis_url,
         jobs_prefix, job_id, "--redisexpiry", str(redis_ttl), str(speciesid),
-        filetype, f"{client.application.config['UPLOAD_FOLDER']}/{filename}"])
+        filetype, f"{client.application.config['UPLOADS_DIRECTORY']}/{filename}"])
 
 @pytest.mark.parametrize(
     "filename,uri,error_msgs",
diff --git a/uploader/expression_data/dbinsert.py b/uploader/expression_data/dbinsert.py
index 6d8ce80..7040698 100644
--- a/uploader/expression_data/dbinsert.py
+++ b/uploader/expression_data/dbinsert.py
@@ -94,7 +94,7 @@ def select_platform():
         job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
         if job:
             filename = job["filename"]
-            filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+            filepath = f"{app.config['UPLOADS_DIRECTORY']}/{filename}"
             if os.path.exists(filepath):
                 default_species = 1
                 gchips = genechips()
@@ -367,7 +367,7 @@ def insert_data():
         assert form.get("datasetid"), "dataset"
 
         filename = form["filename"]
-        filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+        filepath = f"{app.config['UPLOADS_DIRECTORY']}/{filename}"
         redisurl = app.config["REDIS_URL"]
         if os.path.exists(filepath):
             with Redis.from_url(redisurl, decode_responses=True) as rconn:
@@ -377,7 +377,7 @@ def insert_data():
                         form["species"], form["genechipid"], form["datasetid"],
                         app.config["SQL_URI"], redisurl,
                         app.config["JOBS_TTL_SECONDS"]),
-                    redisurl, f"{app.config['UPLOAD_FOLDER']}/job_errors")
+                    redisurl, f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
 
             return redirect(url_for("dbinsert.insert_status", job_id=job["jobid"]))
         return render_error(f"File '{filename}' no longer exists.")
diff --git a/uploader/expression_data/views.py b/uploader/expression_data/views.py
index 0b318b7..0e9b072 100644
--- a/uploader/expression_data/views.py
+++ b/uploader/expression_data/views.py
@@ -162,7 +162,7 @@ def upload_file(species_id: int, population_id: int):
                                    species=species,
                                    population=population)
 
-        upload_dir = app.config["UPLOAD_FOLDER"]
+        upload_dir = app.config["UPLOADS_DIRECTORY"]
         request_errors = errors(request)
         if request_errors:
             for error in request_errors:
@@ -225,7 +225,7 @@ def parse_file(species_id: int, population_id: int):
         _errors = True
 
     if filename:
-        filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename)
+        filepath = os.path.join(app.config["UPLOADS_DIRECTORY"], filename)
         if not os.path.exists(filepath):
             flash("Selected file does not exist (any longer)", "alert-danger")
             _errors = True
@@ -241,7 +241,7 @@ def parse_file(species_id: int, population_id: int):
                 species_id, filepath, filetype,# type: ignore[arg-type]
                 app.config["JOBS_TTL_SECONDS"]),
             redisurl,
-            f"{app.config['UPLOAD_FOLDER']}/job_errors")
+            f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
 
     return redirect(url_for("species.populations.expression-data.parse_status",
                             species_id=species_id,
@@ -263,7 +263,7 @@ def parse_status(species_id: int, population_id: int, job_id: str):
             return render_template("no_such_job.html", job_id=job_id), 400
 
     error_filename = jobs.error_filename(
-        job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
+        job_id, f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
     if os.path.exists(error_filename):
         stat = os.stat(error_filename)
         if stat.st_size > 0:
@@ -345,7 +345,7 @@ def fail(species_id: int, population_id: int, job_id: str):
 
     if job:
         error_filename = jobs.error_filename(
-            job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
+            job_id, f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
         if os.path.exists(error_filename):
             stat = os.stat(error_filename)
             if stat.st_size > 0:
diff --git a/uploader/flask_extensions.py b/uploader/flask_extensions.py
index 83d25aa..226b225 100644
--- a/uploader/flask_extensions.py
+++ b/uploader/flask_extensions.py
@@ -11,7 +11,7 @@ from flask import (
 logger = logging.getLogger(__name__)
 
 
-def __fetch_flags__():
+def fetch_flags():
     flags = {}
     for flag in app.config["FEATURE_FLAGS_HTTP"]:
         flag_value = (request.args.get(flag) or request.form.get(flag) or "").strip()
@@ -38,7 +38,7 @@ def url_for(
                          _scheme=_scheme,
                          _external=_external,
                          **values,
-                         **__fetch_flags__())
+                         **fetch_flags())
 
 
 def render_template(template_name_or_list, **context: Any) -> str:
@@ -47,5 +47,5 @@ def render_template(template_name_or_list, **context: Any) -> str:
         template_name_or_list,
         **{
             **context,
-            **__fetch_flags__() # override any flag values
+            **fetch_flags() # override any flag values
         })
diff --git a/uploader/oauth2/client.py b/uploader/oauth2/client.py
index 4e81afd..e37816d 100644
--- a/uploader/oauth2/client.py
+++ b/uploader/oauth2/client.py
@@ -4,7 +4,7 @@ import time
 import uuid
 import random
 from datetime import datetime, timedelta
-from urllib.parse import urljoin, urlparse
+from urllib.parse import urljoin, urlparse, urlencode
 
 import requests
 from flask import request, current_app as app
@@ -18,6 +18,7 @@ from authlib.integrations.requests_client import OAuth2Session
 
 from uploader import session
 import uploader.monadic_requests as mrequests
+from uploader.flask_extensions import fetch_flags
 
 SCOPE = ("profile group role resource register-client user masquerade "
          "introspect migrate-data")
@@ -176,11 +177,13 @@ def authserver_authorise_uri():
     """Build up the authorisation URI."""
     req_baseurl = urlparse(request.base_url, scheme=request.scheme)
     host_uri = f"{req_baseurl.scheme}://{req_baseurl.netloc}/"
-    return urljoin(
-        authserver_uri(),
-        "auth/authorise?response_type=code"
-        f"&client_id={oauth2_clientid()}"
-        f"&redirect_uri={urljoin(host_uri, 'oauth2/code')}")
+    args = {
+        "response_type": "code",
+        "client_id": oauth2_clientid(),
+        "redirect_uri": (
+            f"{urljoin(host_uri, 'oauth2/code')}?{urlencode(fetch_flags())}")
+    }
+    return f"{urljoin(authserver_uri(), 'auth/authorise')}?{urlencode(args)}"
 
 
 def __no_token__(_err) -> Left:
diff --git a/uploader/population/rqtl2.py b/uploader/population/rqtl2.py
index 97d4854..bb5066e 100644
--- a/uploader/population/rqtl2.py
+++ b/uploader/population/rqtl2.py
@@ -134,7 +134,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
         try:
             app.logger.debug("Files in the form: %s", request.files)
             the_file = save_file(request.files["rqtl2_bundle_file"],
-                                 Path(app.config["UPLOAD_FOLDER"]))
+                                 Path(app.config["UPLOADS_DIRECTORY"]))
         except AssertionError:
             app.logger.debug(traceback.format_exc())
             flash("Please provide a valid R/qtl2 zip bundle.",
@@ -185,7 +185,7 @@ def trigger_rqtl2_bundle_qc(
                     "rqtl2-bundle-file": str(rqtl2bundle.absolute()),
                     "original-filename": originalfilename})}),
             redisuri,
-            f"{app.config['UPLOAD_FOLDER']}/job_errors")
+            f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
         return jobid
 
 
@@ -895,7 +895,7 @@ def confirm_bundle_details(species_id: int, population_id: int):
                         })
                     }),
                 redisuri,
-                f"{app.config['UPLOAD_FOLDER']}/job_errors")
+                f"{app.config['UPLOADS_DIRECTORY']}/job_errors")
 
             return redirect(url_for("expression-data.rqtl2.rqtl2_processing_status",
                                     jobid=jobid))
diff --git a/uploader/samples/views.py b/uploader/samples/views.py
index ee002ba..2a09f8e 100644
--- a/uploader/samples/views.py
+++ b/uploader/samples/views.py
@@ -138,7 +138,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma
 
     try:
         samples_file = save_file(request.files["samples_file"],
-                                 Path(app.config["UPLOAD_FOLDER"]))
+                                 Path(app.config["UPLOADS_DIRECTORY"]))
     except AssertionError:
         flash("You need to provide a file with the samples data.",
               "alert-error")
@@ -172,12 +172,33 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma
                 ] + (["--firstlineheading"] if firstlineheading else []),
                 "samples_upload",
                 extra_meta={
-                    "job_name": f"Samples Upload: {samples_file.name}"
+                    "job_name": f"Samples Upload: {samples_file.name}",
+                    "species_id": species["SpeciesId"],
+                    "population_id": population["Id"],
+                    "success_handler": (
+                        "uploader.samples.views.samples_upload_success_handler")
                 },
                 external_id=session.logged_in_user_id()),
             _jobs_db,
-            Path(f"{app.config['UPLOAD_FOLDER']}/job_errors").absolute(),
+            Path(f"{app.config['UPLOADS_DIRECTORY']}/job_errors").absolute(),
             loglevel=logging.getLevelName(
                 app.logger.getEffectiveLevel()).lower())
         return redirect(
             url_for("background-jobs.job_status", job_id=job["job_id"]))
+
+
+def samples_upload_success_handler(job):
+    """Handler for background jobs: Successful upload of samples"""
+    return return_to_samples_list_view_handler(
+        job, "Samples uploaded successfully.")
+
+
+def return_to_samples_list_view_handler(job, msg):
+    """Handler for background jobs: Return to list_samples page."""
+    flash(msg, "alert alert-success")
+    return redirect(url_for(
+        "species.populations.samples."
+        "list_samples",
+        species_id=job["metadata"]["species_id"],
+        population_id=job["metadata"]["population_id"],
+        job_id=job["job_id"]))
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-02-11 00:10:44 +0000