From 023618f5560a63eab94927f1c361f587fd1b2873 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 25 Jul 2024 14:52:58 -0500
Subject: Fix typing and linting errors.

---
 mypy.ini                      |  9 +++++++++
 scripts/qc_on_rqtl2_bundle.py | 14 +++++++++-----
 uploader/__init__.py          |  2 +-
 3 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/mypy.ini b/mypy.ini
index 08e896e..79c9a9c 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -28,4 +28,13 @@ ignore_missing_imports = True
 ignore_missing_imports = True
 
 [mypy-yaml.*]
+ignore_missing_imports = True
+
+[mypy-pymonad.tools]
+ignore_missing_imports = True
+
+[mypy-pymonad.either]
+ignore_missing_imports = True
+
+[mypy-authlib.*]
 ignore_missing_imports = True
\ No newline at end of file
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
index 150fbce..7784c06 100644
--- a/scripts/qc_on_rqtl2_bundle.py
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -133,7 +133,7 @@ def qc_geno_errors(rconn, fqjobid, _dburi, _speciesid, zfile, logger) -> bool:
 
 def fetch_db_geno_samples(conn: mdb.Connection, speciesid: int) -> tuple[str, ...]:
     """Fetch samples/cases/individuals from the database."""
-    samples = set()
+    samples = set()# type: ignore[var-annotated]
     with conn.cursor() as cursor:
         cursor.execute("SELECT Name, Name2 from Strain WHERE SpeciesId=%s",
                        (speciesid,))
@@ -191,12 +191,13 @@ def check_pheno_samples(
     return allerrors
 
 
-def qc_pheno_errors(rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool:
+def qc_pheno_errors(# pylint: disable=[too-many-arguments]
+        rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool:
     """Check for errors in `pheno` file(s)."""
     cdata = rqtl2.control_data(zfile)
     if "pheno" in cdata:
         logger.info("Checking for errors in the 'pheno' file…")
-        perrs = tuple()
+        perrs = tuple()# type: ignore[var-annotated]
         with database_connection(dburi) as dbconn:
             perrs = check_pheno_samples(
                 dbconn, speciesid, zfile.filename, logger) + tuple(
@@ -216,7 +217,8 @@ def qc_pheno_errors(rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool:
 
     return False
 
-def qc_phenose_errors(rconn, fqjobid, dburi, speciesid, zfile, logger) -> bool:
+def qc_phenose_errors(# pylint: disable=[too-many-arguments]
+        rconn, fqjobid, _dburi, _speciesid, zfile, logger) -> bool:
     """Check for errors in `phenose` file(s)."""
     cdata = rqtl2.control_data(zfile)
     if "phenose" in cdata:
@@ -258,7 +260,9 @@ def run_qc(rconn: Redis,
         if qc_missing_files(rconn, fqjobid, zfile, logger):
             return 1
 
-    def with_zipfile(rconn, fqjobid, dbconn, speciesid, filename, logger, func):
+    def with_zipfile(# pylint: disable=[too-many-arguments]
+            rconn, fqjobid, dbconn, speciesid, filename, logger, func
+    ):
         with ZipFile(filename, "r") as zfile:
             return func(rconn, fqjobid, dbconn, speciesid, zfile, logger)
 
diff --git a/uploader/__init__.py b/uploader/__init__.py
index 3ee8aa0..e9875cf 100644
--- a/uploader/__init__.py
+++ b/uploader/__init__.py
@@ -34,7 +34,7 @@ def create_app():
         app.config.from_envvar("QCAPP_SECRETS")
 
     # setup jinja2 symbols
-    app.jinja_env.globals.update(request_url=lambda : request.url)
+    app.add_template_global(lambda : request.url, name="request_url")
 
     # setup blueprints
     app.register_blueprint(base, url_prefix="/")
-- 
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