Version 1.7.5

flask-app/!!build__dist_pyinstaller.bat

@@ -17,10 +17,12 @@ choice /C AN /M "Clean build ?  A/N"
 if errorlevel 1 set buildClean=--clean
 if errorlevel 2 set buildClean=
 
+echo.
 choice /C AN /M "Test run ?  A/N"
 if errorlevel 1 set testRun=1
 if errorlevel 2 set testRun=0
 
+echo.
 echo Build using pyinstaller : %python%
 
 set srcDir=application

flask-app/.vscode/launch.json

@@ -52,7 +52,7 @@
             },
             "args": [
                 //"--port", "80",
-                //"--config", "conf/mtw.ini",
+                "--config", "conf/mtw.ini",
                 //"--config", "conf/mtw-fr.ini",
                 "--debug",
                 "--fqdn=test.medvik.cz",
@@ -72,7 +72,7 @@
             },
             "args": [
                 //"--port", "5903",
-                //"--config", "conf/mtw.ini",
+                "--config", "conf/mtw.ini",
                 //"--config", "conf/mtw-fr.ini",
                 "--debug"
                 //"--relax"

flask-app/application/logger.py

@@ -0,0 +1,27 @@
+import logging
+from application.modules import utils as mtu
+
+
+def configure_log(app, logname: str = "app"):
+
+    if any(isinstance(h, logging.FileHandler) for h in app.logger.handlers):
+        return
+
+    if app.debug:
+        level = logging.DEBUG
+        log_file = mtu.get_instance_dir(app, f"logs/{logname}_debug.log")
+    else:
+        level = logging.INFO
+        log_file = mtu.get_instance_dir(app, f"logs/{logname}.log")
+
+    app.logger.setLevel(level)
+    app.logger.propagate = False
+
+    formatter = mtu.SafeFormatter("%(asctime)s - %(levelname)s: [%(ip)s] %(message)s")
+
+    handler = logging.FileHandler(log_file, encoding="utf-8")
+    handler.setLevel(level)
+    handler.setFormatter(formatter)
+    handler.addFilter(mtu.RequestIPFilter())
+
+    app.logger.addHandler(handler)

flask-app/application/main.py

@@ -2,8 +2,8 @@
 """
 MeSH Traslation Workflow (MTW) - Flask app factory
 """
+
 import datetime
-import logging
 import os
 from flask import Flask
 from cachelib import FileSystemCache
@@ -21,7 +21,6 @@
 
 def create_app(
     debug=False,
-    logger=None,
     port=5900,
     config_path="conf/mtw.ini",
     server_name=None,
@@ -52,33 +51,11 @@ def create_app(
     if app.debug:
         print("MTW Config:  ", config_path, " - port: ", port)
 
-    if logger:
-        app.logger = logger
-
-    if not app.debug:
-        file_handler = logging.FileHandler(
-            mtu.get_instance_dir(app, "logs/mtw_server.log")
-        )
-        file_handler.setLevel(logging.INFO)
-        file_handler.setFormatter(
-            logging.Formatter("%(asctime)s %(levelname)s: %(message)s ")
-        )
-        app.logger.addHandler(file_handler)
-    else:
-        file_handler = logging.FileHandler(
-            mtu.get_instance_dir(app, "logs/mtw_server_debug.log")
-        )
-        file_handler.setLevel(logging.DEBUG)
-        file_handler.setFormatter(
-            logging.Formatter("%(asctime)s %(levelname)s: %(message)s ")
-        )
-        app.logger.addHandler(file_handler)
-
     app.config.update(
         dict(
             APPLICATION_ROOT=url_prefix,
             APP_NAME="MTW",
-            APP_VER="1.7.4",
+            APP_VER="1.7.5",
             API_VER="1.0.0",
             DBVERSION=1.0,
             CACHE_DIR=mtu.get_instance_dir(app, "cache"),

flask-app/application/modules/auth.py

@@ -54,7 +54,7 @@ def check_public(*args, **kwargs):
                         print(code, msg)
 
                     if code != 200:
-                        app.logger.error(msg)
+                        app.logger.error(f"[check_public] {msg}")
                         abort(403)
 
             return f(*args, **kwargs)
@@ -81,7 +81,7 @@ def validateBasicAuth():
             return True
 
     if has_app_context():
-        app.logger.error("Basic Auth failed")
+        app.logger.error("[validateBasicAuth] failed")
 
 
 def getReqHost():

flask-app/application/modules/database.py

@@ -2,6 +2,7 @@
 """
 MeSH Traslation Workflow (MTW) - database ops
 """
+
 import uuid
 from sqlite3 import dbapi2 as sqlite3
 
@@ -10,7 +11,6 @@
 
 from application.modules.auth import hash_pwd
 
-
 #  Database
 
 
@@ -25,10 +25,10 @@ def get_db():
         try:
             g.sqlite_db = connect_db()
             # g.sqlite_db.execute('pragma foreign_keys=on')
-        except sqlite3.Error as e:
-            error = "Flask get_db error : " + str(e.args[0])
+        except sqlite3.Error as err:
+            error = "Flask get_db error : " + str(err.args[0])
             flash(error, "danger")
-            app.logger.error(error)
+            app.logger.error(f"[get_db] {err}")
             return None
         else:
             return g.sqlite_db

flask-app/application/modules/extensions.py

@@ -2,6 +2,7 @@
 """
 Flask Extensions
 """
+
 from flask_caching import Cache
 
 # from flask_limiter import Limiter

flask-app/application/modules/filters.py

@@ -4,7 +4,6 @@
 from flask import current_app as app
 from application.modules import utils as mtu
 
-
 # Filters & Context processors
 
 

flask-app/application/modules/routes.py

@@ -2,6 +2,7 @@
 """
 Routes & pages
 """
+
 import bcrypt
 import json
 import pprint
@@ -162,9 +163,6 @@ def settings():
     return redirect(ref_redirect())
 
 
-#  Audit
-
-
 @app.route("/todo/", defaults={"tlist": "Preferred"}, methods=["GET"])
 @app.route("/todo/list:<tlist>", methods=["GET"])
 @login_required
@@ -190,6 +188,7 @@ def todo(tlist):
             # pp.pprint(data)
             hits = sparql.parseSparqlData(data)
             # pp.pprint(hits)
+
     else:
         session.pop("tlist", None)
         tlist = "Select a list"
@@ -479,7 +478,7 @@ def update_concept(dui, pref):
             else:
                 msg = "Operation FAILED for Concept : " + concept
                 flash(msg, "danger")
-                app.logger.error(msg)
+                app.logger.error(f"[update_concept] {msg}")
 
     return redirect(url_for("search", dui=dui))
 
@@ -525,7 +524,7 @@ def add_cpid(dui, cui):
                     check = False
                     msg = "CUI already exist ! "
                     flash(msg, "danger")
-                    app.logger.error(msg + cpid + " for " + curi)
+                    app.logger.error(f"[add_cpid] {msg} : {cpid} for {curi}")
                     return redirect(ref_redirect())
         if check:
             updated = sparql.updateTriple(
@@ -554,11 +553,11 @@ def add_cpid(dui, cui):
             )
             msg = "CUI generated: " + cpid
             flash(msg, "info")
-            app.logger.info(msg + " for " + curi)
+            app.logger.info(f"[add_cpid] {msg} : {cpid} for {curi}")
         else:
             msg = "CUI update FAILED ! "
             flash(msg, "danger")
-            app.logger.error(msg + cpid + " for " + curi)
+            app.logger.error(f"[add_cpid] {msg} : {cpid} for {curi}")
 
     else:
         msg = "CUI already issued - please try again"
@@ -574,6 +573,7 @@ def update_note(dui):
     if session["ugroup"] in ["viewer", "disabled", "locked"]:
         msg = "Insufficient priviledges"
         flash(msg, "warning")
+        app.logger.warning(f"[update_note] {dui} : {msg}")
         return render_template("errors/error_page.html", errcode=403, error=msg), 403
 
     if request.form.get("predicate") and request.form.get("label"):
@@ -582,9 +582,9 @@ def update_note(dui):
         label = request.form["label"].replace("?", "").strip()
 
         if predicate not in app.config["DESC_NOTES"]:
-            msg = "Update note: Unknown mesht predicate"
+            msg = "Unknown mesht: predicate"
             flash(msg, "danger")
-            app.logger.error(msg)
+            app.logger.error(f"[update_note] {msg}")
             return (
                 render_template("errors/error_page.html", errcode=403, error=msg),
                 403,
@@ -1011,9 +1011,6 @@ def update_audit():
             return redirect(url_for("search", dui=dui, tab="history"))
 
 
-#  Compare
-
-
 @app.route("/compare/", defaults={"dui": ""}, methods=["GET"])
 @app.route("/compare/dui:<dui>", methods=["GET"])
 @login_required
@@ -1063,9 +1060,6 @@ def compare(dui):
     )
 
 
-#  Audit
-
-
 @app.route("/audit/", defaults={"dui": "", "cui": ""}, methods=["GET"])
 @app.route("/audit/dui:<dui>", defaults={"cui": ""}, methods=["GET"])
 @app.route("/audit/dui:<dui>/cui:<cui>", methods=["GET"])
@@ -1105,9 +1099,6 @@ def audit(dui, cui):
     )
 
 
-#  Approval
-
-
 @app.route(
     "/approve/",
     defaults={"userid": "", "username": "", "status": "", "event": ""},
@@ -1489,16 +1480,17 @@ def search(dui, action):
     if text_query:
         data = sparql.getSparqlData(
             "search",
+            # "search_old",
             query=text_query,
             show=session.get("sshow"),
             status=session.get("sstatus"),
             slang=session.get("slang"),
             scr=session.get("scr"),
             qtp=session.get("qtp"),
         )
-        # pp.pprint(data)
-
         if data:
+            # if app.debug:
+            #    app.logger.error(json.dumps(data))
             started = timer()
             hits = sparql.parseSparqlData(data)
             # pp.pprint(hits)
@@ -1565,9 +1557,6 @@ def store_visited(dui, label):
                 del session["visited"][rem]
 
 
-#  Reporting
-
-
 @app.route("/report/", defaults={"userid": "", "year": ""}, methods=["GET"])
 @app.route("/report/userid:<userid>", defaults={"year": ""}, methods=["GET"])
 @app.route("/report/year:<year>", defaults={"userid": ""}, methods=["GET"])
@@ -1672,9 +1661,6 @@ def report(userid, year):
         )
 
 
-#  Management
-
-
 @app.route("/manage/", defaults={"action": ""}, methods=["GET"])
 @app.route("/manage/action:<action>", methods=["POST"])
 @login_required
@@ -1773,7 +1759,7 @@ def manage(action):
             exp_files[f]["fname"] = fp.name
             exp_files[f]["fdate"] = mtu.getFpathDate(fp)
 
-    # 2024_umls.tsv
+    # YYYY_umls.tsv
     show_umls_exports = False
     umls_tsv = mtu.getTempFpath("umls", ext="tsv")
     if umls_tsv.is_file():
@@ -2056,9 +2042,6 @@ def update_user():
         return redirect(url_for("manage"))
 
 
-#  Login | Logout
-
-
 @app.route("/login/", methods=["GET", "POST"])
 # @limiter.limit("10/minute")
 def login():

flask-app/application/modules/sparql.py

@@ -2,6 +2,7 @@
 """
 MeSH Traslation Workflow (MTW) - SPARQL ops
 """
+
 import datetime
 import requests
 import pprint
@@ -108,6 +109,7 @@ def getSparqlData(
                 endpoint, headers=headers, data=sparql.encode("utf-8"), timeout=600
             )
         ) as r:
+            r.raise_for_status()
             show_elapsed(t0, tag="result ready: " + template)
             if r.status_code == 200:
                 if output == "json":
@@ -126,6 +128,9 @@ def getSparqlData(
             "%s \n\n %s \n\n %s \n\n %s", endpoint, template, query, str(err)
         )
 
+    except Exception as err:
+        app.logger.error(f"[getSparqlData] {err}")
+
 
 def getSparqlDataExt(dui, output, year="", key=None, cache=None, otype="Descriptor"):