From 7338adaef330f9caf734b8a8e586fc980b34d256 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Thu, 24 Oct 2024 15:46:12 +0000
Subject: [PATCH 01/57] Store all requests to pages hosted by BugHog and minor
 fixes

---
 bci/evaluations/collectors/base.py     | 21 ++++---------
 bci/evaluations/collectors/requests.py | 41 +++++++++++++++++++-------
 bci/web/blueprints/experiments.py      | 25 ++++++----------
 bci/web/templates/cookies.html         | 13 +++++---
 nginx/config/experiments.conf          | 10 +++++++
 nginx/config/notify_collector.conf     | 30 +++++++++++++++++++
 6 files changed, 93 insertions(+), 47 deletions(-)
 create mode 100644 nginx/config/notify_collector.conf

diff --git a/bci/evaluations/collectors/base.py b/bci/evaluations/collectors/base.py
index 903ed5d2..b85ee6f5 100644
--- a/bci/evaluations/collectors/base.py
+++ b/bci/evaluations/collectors/base.py
@@ -3,23 +3,22 @@
 
 
 class BaseCollector:
-
     def __init__(self) -> None:
         self.data = {}
 
     @abstractmethod
-    def start():
+    def start(self):
         pass
 
     @abstractmethod
-    def stop():
+    def stop(self):
         pass
 
     @staticmethod
     def _parse_bughog_variables(raw_log_lines: list[str], regex) -> list[tuple[str, str]]:
-        '''
+        """
         Parses the given `raw_log_lines` for matches against the given `regex`.
-        '''
+        """
         data = []
         regex_match_lists = [re.findall(regex, line) for line in raw_log_lines if re.search(regex, line)]
         # Flatten list
@@ -27,15 +26,5 @@ def _parse_bughog_variables(raw_log_lines: list[str], regex) -> list[tuple[str,
         for match in regex_matches:
             var = match[0]
             val = match[1]
-            BaseCollector._add_val_var_pair(var, val, data)
+            data.append({'var': var, 'val': val})
         return data
-
-    @staticmethod
-    def _add_val_var_pair(var: str, val: str, data: list) -> list:
-        for entry in data:
-            if entry['var'] == var and entry['val'] == val:
-                return data
-        data.append({
-            'var': var,
-            'val': val
-        })
diff --git a/bci/evaluations/collectors/requests.py b/bci/evaluations/collectors/requests.py
index d5b9efe3..1e6906ba 100644
--- a/bci/evaluations/collectors/requests.py
+++ b/bci/evaluations/collectors/requests.py
@@ -1,6 +1,7 @@
 import http.server
 import json
 import logging
+import socket
 import socketserver
 from threading import Thread
 
@@ -12,32 +13,49 @@
 
 
 class RequestHandler(http.server.BaseHTTPRequestHandler):
+    """
+    Handles requests sent to the collector.
+    """
 
     def __init__(self, collector, request, client_address, server) -> None:
         self.collector = collector
         self.request_body = None
         super().__init__(request, client_address, server)
 
-    def log_message(self, *_):
+    def log_message(self, format: str, *args) -> None:
+        """
+        Handle and store the received body.
+        """
         if not self.request_body:
             logger.debug('Received request without body')
             return
 
-        logger.debug(f'Received request with body: {self.request_body}')
         request_body = json.loads(self.request_body)
+        logger.debug(f'Received request information with {len(request_body.keys())} attributes.')
         self.collector.data['requests'].append(request_body)
 
     def do_POST(self):
-        content_length = int(self.headers['Content-Length'])
-        body = self.rfile.read(content_length)
-        self.request_body = body.decode('utf-8')
-        self.send_response(200)
-        self.end_headers()
-        self.wfile.write(b'Post request received')
+        """
+        This function is called upon receiving a POST request.
+        It sets `self.request_body`, which will be parsed later by `self.log_message`.
+        """
+        # We have to read the body before allowing it to be thrashed when connection clusure is confirmed.
+        if self.headers['Content-Length'] is not None:
+            content_length = int(self.headers['Content-Length'])
+            body = self.rfile.read(content_length)
+            self.request_body = body.decode('utf-8')
 
+        # Because of our hacky NGINX methodology, we have to allow premature socket closings.
+        try:
+            self.send_response(200)
+            self.send_header('Content-Type', 'text/plain; charset=utf-8')
+            self.end_headers()
+            self.wfile.write('Post request received!\n'.encode('utf-8'))
+        except socket.error:
+            logger.debug('Socket closed by NGINX (expected)')
 
-class RequestCollector(BaseCollector):
 
+class RequestCollector(BaseCollector):
     def __init__(self):
         super().__init__()
         self.__httpd = None
@@ -48,7 +66,7 @@ def __init__(self):
     def start(self):
         logger.debug('Starting collector...')
         socketserver.TCPServer.allow_reuse_address = True
-        self.__httpd = socketserver.TCPServer(("", PORT), lambda *args, **kwargs: RequestHandler(self, *args, **kwargs))
+        self.__httpd = socketserver.TCPServer(('', PORT), lambda *args, **kwargs: RequestHandler(self, *args, **kwargs))
         # self.__httpd.allow_reuse_address = True
         self.__thread = Thread(target=self.__httpd.serve_forever)
         self.__thread.start()
@@ -58,7 +76,8 @@ def stop(self):
         regex = r'bughog_(.+)=(.+)'
         if self.__httpd:
             self.__httpd.shutdown()
-            self.__thread.join()
+            if self.__thread:
+                self.__thread.join()
             self.__httpd.server_close()
         request_urls = [request['url'] for request in self.data['requests'] if 'url' in request]
         data = self._parse_bughog_variables(request_urls, regex)
diff --git a/bci/web/blueprints/experiments.py b/bci/web/blueprints/experiments.py
index 96297cc1..5ef7af53 100644
--- a/bci/web/blueprints/experiments.py
+++ b/bci/web/blueprints/experiments.py
@@ -39,17 +39,10 @@ def index():
 
 @exp.route("/report/", methods=["GET", "POST"])
 def report():
-    leak = request.args.get("leak")
-    if leak is not None:
-        resp = make_response(
-            render_template("cookies.html", title="Report", to_report=leak)
-        )
-    else:
-        resp = make_response(
-            render_template(
-                "cookies.html", title="Report", to_report="Nothing to report"
-            )
-        )
+    get_params = [item for item in get_all_GET_parameters(request).items()]
+    resp = make_response(
+        render_template("cookies.html", title="Report", get_params=get_params)
+    )
 
     cookie_exp_date = datetime.datetime.now() + datetime.timedelta(weeks=4)
     resp.set_cookie("generic", "1", expires=cookie_exp_date)
@@ -86,7 +79,7 @@ def report_leak_if_using_http(target_scheme):
     Triggers request to /report/ if a request was received over the specified `scheme`.
     """
     used_scheme = request.headers.get("X-Forwarded-Proto")
-    params = get_all_bughog_GET_parameters(request)
+    params = get_all_GET_parameters(request)
     if used_scheme == target_scheme:
         return "Redirect", 307, {"Location": url_for("experiments.report", **params)}
     else:
@@ -101,7 +94,7 @@ def report_leak_if_present(expected_header_name: str):
     if expected_header_name not in request.headers:
         return f"Header {expected_header_name} not found", 200, {"Allow-CSP-From": "*"}
 
-    params = get_all_bughog_GET_parameters(request)
+    params = get_all_GET_parameters(request)
     return (
         "Redirect",
         307,
@@ -126,7 +119,7 @@ def report_leak_if_contains(expected_header_name: str, expected_header_value: st
             {"Allow-CSP-From": "*"},
         )
 
-    params = get_all_bughog_GET_parameters(request)
+    params = get_all_GET_parameters(request)
     return (
         "Redirect",
         307,
@@ -137,5 +130,5 @@ def report_leak_if_contains(expected_header_name: str, expected_header_value: st
     )
 
 
-def get_all_bughog_GET_parameters(request):
-    return {k: v for k, v in request.args.items() if k.startswith("bughog_")}
+def get_all_GET_parameters(request):
+    return {k: v for k, v in request.args.items()}
diff --git a/bci/web/templates/cookies.html b/bci/web/templates/cookies.html
index 320a3907..2e1b0b0c 100644
--- a/bci/web/templates/cookies.html
+++ b/bci/web/templates/cookies.html
@@ -2,10 +2,15 @@
 
 {% block content %}
 
-{% if to_report %}
+{% if get_params %}
 <h2>Reported: </h2>
-
-<p>{{ to_report }}</p>
+<ul>
+{% for get_param in get_params %}
+    <li>{{ get_param[0] }}: {{ get_param[1] }}</li>
+{% endfor %}
+</ul>
+{% else %}
+No GET parameters.
 {% endif %}
 
 <h2>Cookies</h2>
@@ -20,4 +25,4 @@ <h2>Cookies</h2>
         elem.appendChild(cookie);
     }
 </script>
-{% endblock %}
\ No newline at end of file
+{% endblock %}
diff --git a/nginx/config/experiments.conf b/nginx/config/experiments.conf
index 92c6447c..940b5b9f 100644
--- a/nginx/config/experiments.conf
+++ b/nginx/config/experiments.conf
@@ -1,6 +1,11 @@
 access_log /logs/nginx-access-poc.log default_format;
 
 location /res/ {
+    include /etc/nginx/config/notify_collector.conf;
+    error_page 504 @resources;
+}
+
+location @resources {
     root /www/data;
 }
 
@@ -48,6 +53,11 @@ location ~ ^/(.+)/(.+)/(.+)/$ {
 }
 
 location ~ ^/(.+)/(.+)/(.+)$ {
+    include /etc/nginx/config/notify_collector.conf;
+    error_page 504 @experiment;
+}
+
+location @experiment {
     rewrite ^/(.+)$ /$1/;
 }
 
diff --git a/nginx/config/notify_collector.conf b/nginx/config/notify_collector.conf
new file mode 100644
index 00000000..78bd8fc0
--- /dev/null
+++ b/nginx/config/notify_collector.conf
@@ -0,0 +1,30 @@
+# We want to notify worker-specific request collectors of every request to our experiment server.
+# Hacky solution: pretend that the collector is not reachable and use fallback to serve experiment page.
+# So:
+# 1. NGINX will send request to request collector of worker.
+# 2. NGINX will serve the experiment page.
+
+proxy_pass http://$remote_addr:5001/report/;
+proxy_set_header X-Real-IP $remote_addr;
+proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+proxy_set_header X-Forwarded-Proto $scheme;
+
+proxy_method POST;
+proxy_set_header Content-Type "application/json";
+
+set $request_body_data '';
+if ($request_body) {
+    set $request_body_data "$request_body";
+}
+
+set $url '"url": "${scheme}://${host}${request_uri}"';
+set $method '"method": "$request_method"';
+set $content '"content": "${request_body_data}"';
+set $report '{${url}, ${method}, ${content}}';
+proxy_set_body $report;
+
+# We don't need any response, we merely want to notify
+proxy_connect_timeout 2s;
+proxy_send_timeout 2s;
+proxy_read_timeout 0s;  # Force a 504 by setting timeout to 0
+

From bd0e23bb2ca71ab8a43cb689ffa9e822364d5359 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <szymsza@users.noreply.github.com>
Date: Tue, 29 Oct 2024 14:45:44 +0100
Subject: [PATCH 02/57] Custom .py experiment files (#34)

* Fix code highlighting modes and add new .py filetype

* Add empty testing Python server experiment

* Fix Python ace mode

* Fix loading Python files

* Simple Python server fetch experiment

* Basic python directory proxying

* Dynamically import and execute Python experiment files

* Pass request data to custom Python files

* Default Python server template content

* Add JSON highlighting

* Remove python server headers

* Disable creating __pycache__ folder with dynamic imports
---
 bci/evaluations/custom/custom_evaluation.py   | 46 +++++++++++++------
 bci/web/blueprints/experiments.py             | 22 +++++++++
 bci/web/page_parser.py                        |  4 ++
 bci/web/vue/src/components/poc-editor.vue     | 18 ++++++--
 .../PythonServer/a.test/main/headers.json     |  6 +++
 .../PythonServer/a.test/main/index.html       | 11 +++++
 .../PythonServer/a.test/py-server/index.py    | 15 ++++++
 nginx/config/experiments.conf                 |  8 ++++
 8 files changed, 112 insertions(+), 18 deletions(-)
 create mode 100644 experiments/pages/Support/PythonServer/a.test/main/headers.json
 create mode 100644 experiments/pages/Support/PythonServer/a.test/main/index.html
 create mode 100644 experiments/pages/Support/PythonServer/a.test/py-server/index.py

diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index b359c036..279065e3 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -166,27 +166,43 @@ def add_page(self, project: str, poc: str, domain: str, path: str, file_type: st
         if os.path.exists(file_path):
             return False
         with open(file_path, 'w') as file:
-            file.write('')
-        headers_file_path = os.path.join(page_path, 'headers.json')
-        if not os.path.exists(headers_file_path):
-            with open(headers_file_path, 'w') as file:
-                file.write(
-                    textwrap.dedent(
-                        """\
-                        [
-                            {
-                                "key": "Header-Name",
-                                "value": "Header-Value"
-                            }
-                        ]
-                    """
+            file.write(self.get_default_file_content(file_type))
+
+        if self.include_file_headers(file_type):
+            headers_file_path = os.path.join(page_path, 'headers.json')
+            if not os.path.exists(headers_file_path):
+                with open(headers_file_path, 'w') as file:
+                    file.write(
+                        textwrap.dedent(
+                            """\
+                            [
+                                {
+                                    "key": "Header-Name",
+                                    "value": "Header-Value"
+                                }
+                            ]
+                        """
+                        )
                     )
-                )
         self.sync_with_folders()
         # Notify clients of change (an experiment might now be runnable)
         Clients.push_experiments_to_all()
         return True
 
+    @staticmethod
+    def get_default_file_content(file_type: str) -> str:
+        if file_type != 'py':
+            return ''
+
+        with open('experiments/pages/Support/PythonServer/a.test/py-server/index.py', 'r') as file:
+            template_content = file.read()
+
+        return template_content
+
+    @staticmethod
+    def include_file_headers(file_type: str) -> bool:
+        return file_type != 'py'
+
     def sync_with_folders(self):
         self.dir_tree = self.initialize_dir_tree()
         self.tests_per_project = self.initialize_tests_and_url_queues(self.dir_tree)
diff --git a/bci/web/blueprints/experiments.py b/bci/web/blueprints/experiments.py
index 5ef7af53..2de8daeb 100644
--- a/bci/web/blueprints/experiments.py
+++ b/bci/web/blueprints/experiments.py
@@ -1,6 +1,8 @@
 import datetime
 import logging
 import threading
+import importlib.util
+import sys
 
 import requests
 from flask import Blueprint, make_response, render_template, request, url_for
@@ -130,5 +132,25 @@ def report_leak_if_contains(expected_header_name: str, expected_header_value: st
     )
 
 
+@exp.route("/<string:project>/<string:experiment>/<string:directory>/")
+def python_evaluation(project: str, experiment: str, directory: str):
+    """
+    Evaluates the python script and returns its result.
+    """
+    host = request.host.lower()
+
+    module_name = f"{host}/{project}/{experiment}/{directory}"
+    path = f"experiments/pages/{project}/{experiment}/{host}/{directory}/index.py"
+
+    # Dynamically import the file
+    sys.dont_write_bytecode = True
+    spec = importlib.util.spec_from_file_location(module_name, path)
+    module = importlib.util.module_from_spec(spec)
+    sys.modules[module_name] = module
+    spec.loader.exec_module(module)
+
+    return module.main(request)
+
+  
 def get_all_GET_parameters(request):
     return {k: v for k, v in request.args.items()}
diff --git a/bci/web/page_parser.py b/bci/web/page_parser.py
index 1cff781d..57dc6186 100644
--- a/bci/web/page_parser.py
+++ b/bci/web/page_parser.py
@@ -68,6 +68,10 @@ def get_content(subdir_folder_path: str):
         {
             "file_name": "index.js",
             "content_type": "text/javascript"
+        },
+        {
+            "file_name": "index.py",
+            "content_type": "text/x-python"
         }
     ]
     content = None
diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 7bac6b8e..59e894fb 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -1,5 +1,9 @@
 <script>
   import ace from "ace-builds";
+  import { Mode as HtmlMode } from 'ace-builds/src-noconflict/mode-html';
+  import { Mode as JsMode } from 'ace-builds/src-noconflict/mode-javascript';
+  import { Mode as JsonMode } from 'ace-builds/src-noconflict/mode-json';
+  import { Mode as PyMode } from 'ace-builds/src-noconflict/mode-python';
   import 'ace-builds/src-min-noconflict/ext-modelist';
   import 'ace-builds/src-min-noconflict/theme-twilight';
   import 'ace-builds/src-min-noconflict/theme-xcode';
@@ -38,6 +42,7 @@
         available_file_types: [
           'html',
           'js',
+          'py',
         ],
         dialog: {
           domain: {
@@ -73,6 +78,7 @@
             this.editor.setValue(res.data.content);
             this.editor.clearSelection();
             this.active_file.should_update_server = true;
+            this.update_editor_mode(file_name);
           }
         })
         .catch((error) => {
@@ -123,13 +129,19 @@
         });
       },
       update_editor_mode(file_name) {
-        file_ext = file_name.split('.').pop();
+        const file_ext = file_name.split('.').pop();
         switch (file_ext) {
           case "html":
-            this.editor.session.setMode("ace/mode/html");
+            this.editor.session.setMode(new HtmlMode());
             break;
           case "js":
-            this.editor.session.setMode("ace/mode/js");
+            this.editor.session.setMode(new JsMode());
+            break;
+          case "json":
+            this.editor.session.setMode(new JsonMode());
+            break;
+          case "py":
+            this.editor.session.setMode(new PyMode());
             break;
         }
       },
diff --git a/experiments/pages/Support/PythonServer/a.test/main/headers.json b/experiments/pages/Support/PythonServer/a.test/main/headers.json
new file mode 100644
index 00000000..270dd21c
--- /dev/null
+++ b/experiments/pages/Support/PythonServer/a.test/main/headers.json
@@ -0,0 +1,6 @@
+[
+    {
+        "key": "Header-Name",
+        "value": "Header-Value"
+    }
+]
diff --git a/experiments/pages/Support/PythonServer/a.test/main/index.html b/experiments/pages/Support/PythonServer/a.test/main/index.html
new file mode 100644
index 00000000..e2d4e786
--- /dev/null
+++ b/experiments/pages/Support/PythonServer/a.test/main/index.html
@@ -0,0 +1,11 @@
+<html>
+    <body>
+        <script>
+            (async () => {
+                const res = await fetch('https://a.test/Support/PythonServer/py-server/');
+                const x = await res.text();
+                document.location = `https://a.test/report/?leak=PythonServer&response=${encodeURIComponent(JSON.stringify(x))}`;
+            })();
+        </script>
+    </body>
+</html>
\ No newline at end of file
diff --git a/experiments/pages/Support/PythonServer/a.test/py-server/index.py b/experiments/pages/Support/PythonServer/a.test/py-server/index.py
new file mode 100644
index 00000000..91e823b8
--- /dev/null
+++ b/experiments/pages/Support/PythonServer/a.test/py-server/index.py
@@ -0,0 +1,15 @@
+from flask import Request
+
+# Make sure that your page directory starts with 'py-'
+
+def main(req: Request):
+    # TODO - implement your functionality and return a Flask response
+    
+    return {
+        "agent": req.headers.get("User-Agent"),
+        "cookies": req.cookies,
+        "host": req.host,
+        "path": req.path,
+        "scheme": req.scheme,
+        "url": req.url
+    }
\ No newline at end of file
diff --git a/nginx/config/experiments.conf b/nginx/config/experiments.conf
index 940b5b9f..398dac9c 100644
--- a/nginx/config/experiments.conf
+++ b/nginx/config/experiments.conf
@@ -21,6 +21,14 @@ location ~ ^/report(/.+)*/?$ {
     proxy_set_header X-Forwarded-Proto $scheme;
 }
 
+location ~ ^/(.+)/(.+)/py-(.+)/$ {
+    proxy_pass http://core:5000;
+    proxy_set_header Host $host;
+    proxy_set_header X-Real-IP $remote_addr;
+    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+    proxy_set_header X-Forwarded-Proto $scheme;
+}
+
 location ~ ^/(.+)/(.+)/(.+)/$ {
     root /www/data/pages;
     index index.html index.js;

From 1da8973323608181205163a1ca06409558a02b3a Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Wed, 30 Oct 2024 12:22:54 +0000
Subject: [PATCH 03/57] WiP - interaction script

---
 bci/browser/interaction/__init__.py           |  0
 bci/browser/interaction/browsers/__init__.py  |  0
 bci/browser/interaction/browsers/browser.py   | 82 +++++++++++++++++++
 bci/browser/interaction/browsers/chromium.py  | 51 ++++++++++++
 bci/browser/interaction/browsers/firefox.py   | 74 +++++++++++++++++
 bci/browser/interaction/interaction.py        | 13 +++
 bci/evaluations/custom/custom_evaluation.py   | 51 ++++++++----
 .../UserInteraction/a.test/main/headers.json  |  1 +
 .../UserInteraction/a.test/main/index.html    |  6 ++
 .../UserInteraction/interaction_script.cmd    |  1 +
 requirements.in                               |  1 +
 requirements.txt                              |  4 +-
 12 files changed, 269 insertions(+), 15 deletions(-)
 create mode 100644 bci/browser/interaction/__init__.py
 create mode 100644 bci/browser/interaction/browsers/__init__.py
 create mode 100644 bci/browser/interaction/browsers/browser.py
 create mode 100644 bci/browser/interaction/browsers/chromium.py
 create mode 100644 bci/browser/interaction/browsers/firefox.py
 create mode 100644 bci/browser/interaction/interaction.py
 create mode 100644 experiments/pages/Support/UserInteraction/a.test/main/headers.json
 create mode 100644 experiments/pages/Support/UserInteraction/a.test/main/index.html
 create mode 100644 experiments/pages/Support/UserInteraction/interaction_script.cmd

diff --git a/bci/browser/interaction/__init__.py b/bci/browser/interaction/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/bci/browser/interaction/browsers/__init__.py b/bci/browser/interaction/browsers/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/bci/browser/interaction/browsers/browser.py b/bci/browser/interaction/browsers/browser.py
new file mode 100644
index 00000000..a969fcce
--- /dev/null
+++ b/bci/browser/interaction/browsers/browser.py
@@ -0,0 +1,82 @@
+import json
+from abc import ABC, abstractmethod
+
+from websockets.sync.client import ClientConnection, connect
+
+
+# Returns true if:
+# - required == True -> all fields from `pattern` are present in `data` with the same value
+# - required == False -> all fields from `pattern` which are present in `data` have the same value
+def dictionaries_match(pattern: dict, data: dict, required: bool) -> bool:
+    for key in pattern:
+        if required and key not in data:
+            return False
+
+        if key in data:
+            # Equal values, up to slashes
+            if (
+                not dictionaries_match(pattern[key], data[key], required)
+                if isinstance(pattern[key], dict)
+                else str(data[key]).replace('/', '') != str(pattern[key]).replace('/', '')
+            ):
+                return False
+    return True
+
+
+class Browser(ABC):
+    request_id: int = 0
+    ws_timeout: float
+    ws: ClientConnection
+
+    def __init__(self, browser_id: str = '', port: int = 9222, host: str = '127.0.0.1', autoclose_timeout: float = 0.5):
+        self.ws_timeout = autoclose_timeout
+        self.ws = connect(self.get_ws_endpoint(host, port, browser_id), close_timeout=autoclose_timeout)
+        self.initialize_connection(browser_id, port, host)
+
+    def req_id(self) -> int:
+        self.request_id += 1
+        return self.request_id
+
+    def send(self, data: dict) -> dict:
+        data['id'] = self.req_id()
+
+        self.ws.send(json.dumps(data))
+
+        return self.receive({'method': data['method'], 'id': data['id']}, False)
+
+    def listen(self, event: str, params: dict) -> dict:
+        return self.receive({'type': 'event', 'method': event, 'params': params}, True)
+
+    def receive(self, data: dict, required: bool) -> dict:
+        result = None
+
+        while result == None or (not dictionaries_match(data, result, required)):
+            result = json.loads(self.ws.recv(self.ws_timeout))
+
+            if 'type' in result and result['type'] == 'error':
+                raise Exception(f'Received browser error: {result}')
+
+        return result
+
+    # --- BROWSER-SPECIFIC METHODS ---
+    @abstractmethod
+    def get_ws_endpoint(self, host: str, port: int, browser_id: str) -> str:
+        pass
+
+    @abstractmethod
+    def initialize_connection(self, _browserId, _port, _host):
+        pass
+
+    @abstractmethod
+    def close_connection(
+        self,
+    ):
+        pass
+
+    @abstractmethod
+    def navigate(self, _url):
+        pass
+
+    @abstractmethod
+    def click(self, _x, _y):
+        pass
diff --git a/bci/browser/interaction/browsers/chromium.py b/bci/browser/interaction/browsers/chromium.py
new file mode 100644
index 00000000..b82c7014
--- /dev/null
+++ b/bci/browser/interaction/browsers/chromium.py
@@ -0,0 +1,51 @@
+from time import sleep
+
+from .browser import Browser
+
+
+class Chromium(Browser):
+    session_id: str
+
+    def get_ws_endpoint(self, host: str, port: int, browser_id: str) -> str:
+        return f'ws://{host}:{port}/devtools/browser/{browser_id}'
+
+    def initialize_connection(self, browserId, port, host):
+        # Get list of all targets and find a "page" target.
+        target_response = self.send(
+            {
+                'method': 'Target.getTargets',
+            }
+        )
+
+        page_target = list(filter(lambda info: (info['type'] == 'page'), target_response['result']['targetInfos']))[0][
+            'targetId'
+        ]
+
+        # Attach to the page target.
+        session = self.send({'method': 'Target.attachToTarget', 'params': {'targetId': page_target, 'flatten': True}})
+
+        self.session_id = session['result']['sessionId']
+
+    def close_connection(self):
+        pass
+
+    def navigate(self, url):
+        self.send({'sessionId': self.session_id, 'method': 'Page.navigate', 'params': {'url': url}})
+        sleep(0.01)
+
+    def click(self, x, y):
+        self.send(
+            {
+                'sessionId': self.session_id,
+                'method': 'Input.dispatchMouseEvent',
+                'params': {'x': x, 'y': y, 'type': 'mousePressed', 'clickCount': 1, 'button': 'left'},
+            }
+        )
+
+        self.send(
+            {
+                'sessionId': self.session_id,
+                'method': 'Input.dispatchMouseEvent',
+                'params': {'x': x, 'y': y, 'type': 'mouseReleased', 'button': 'left'},
+            }
+        )
diff --git a/bci/browser/interaction/browsers/firefox.py b/bci/browser/interaction/browsers/firefox.py
new file mode 100644
index 00000000..97dd7202
--- /dev/null
+++ b/bci/browser/interaction/browsers/firefox.py
@@ -0,0 +1,74 @@
+from .browser import Browser
+
+
+class Firefox(Browser):
+    browsing_context: str
+
+    def get_ws_endpoint(self, host: str, port: int, browser_id: str) -> str:
+        return f'ws://{host}:{port}/session'
+
+    def initialize_connection(self, browserId, port, host):
+        # Initiate the session
+        session_id = self.send({'method': 'session.new', 'params': {'capabilities': {}}})['result']['sessionId']
+
+        # Subscribe to browser events
+        self.send(
+            {
+                'method': 'session.subscribe',
+                'params': {
+                    'events': [
+                        'browsingContext.domContentLoaded',
+                    ]
+                },
+            }
+        )
+
+        # Create the browsing context
+        user_context = self.send({'method': 'browser.createUserContext', 'params': {}})['result']['userContext']
+
+        self.browsing_context = self.send(
+            {'method': 'browsingContext.create', 'params': {'type': 'tab', 'userContext': user_context}}
+        )['result']['context']
+
+    def close_connection(self):
+        self.send(
+            {
+                'method': 'session.end',
+                'params': {},
+            }
+        )
+
+    def navigate(self, url):
+        navigation = self.send(
+            {'method': 'browsingContext.navigate', 'params': {'url': url, 'context': self.browsing_context}}
+        )['result']['navigation']
+
+        # Wait for the DOM to load
+        self.listen(
+            'browsingContext.domContentLoaded',
+            {
+                'url': url,
+                'context': self.browsing_context,
+                'navigation': navigation,
+            },
+        )
+
+    def click(self, x, y):
+        self.send(
+            {
+                'method': 'input.performActions',
+                'params': {
+                    'context': self.browsing_context,
+                    'actions': [
+                        {
+                            'type': 'pointer',
+                            'id': str(self.req_id()),
+                            'actions': [
+                                {'type': 'pointerDown', 'button': 1, 'width': x, 'height': y},
+                                {'type': 'pointerUp', 'button': 1, 'width': x, 'height': y},
+                            ],
+                        }
+                    ],
+                },
+            }
+        )
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
new file mode 100644
index 00000000..8a014ac1
--- /dev/null
+++ b/bci/browser/interaction/interaction.py
@@ -0,0 +1,13 @@
+from bci.browser.configuration.browser import Browser as BrowserConfig
+
+
+class Interaction:
+    browser_config: BrowserConfig
+    script: list[str]
+
+    def __init__(self, browser: BrowserConfig, script: list[str]) -> None:
+        self.browser_config = browser
+        self.script = script
+
+    def execute(self) -> None:
+        print(f'TODO - execute {self.browser_config._get_terminal_args()} with script {", ".join(self.script)}')
diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index 279065e3..3f235378 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -3,6 +3,7 @@
 import textwrap
 
 from bci.browser.configuration.browser import Browser
+from bci.browser.interaction.interaction import Interaction
 from bci.configuration import Global
 from bci.evaluations.collectors.collector import Collector, Type
 from bci.evaluations.evaluation_framework import EvaluationFramework
@@ -16,7 +17,7 @@ class CustomEvaluationFramework(EvaluationFramework):
     def __init__(self):
         super().__init__()
         self.dir_tree = self.initialize_dir_tree()
-        self.tests_per_project = self.initialize_tests_and_url_queues(self.dir_tree)
+        self.tests_per_project = self.initialize_tests_and_interactions(self.dir_tree)
 
     @staticmethod
     def initialize_dir_tree() -> dict:
@@ -35,7 +36,7 @@ def path_to_dict(path):
         return path_to_dict(path)
 
     @staticmethod
-    def initialize_tests_and_url_queues(dir_tree: dict) -> dict:
+    def initialize_tests_and_interactions(dir_tree: dict) -> dict:
         experiments_per_project = {}
         page_folder_path = Global.custom_page_folder
         for project, experiments in dir_tree.items():
@@ -43,13 +44,29 @@ def initialize_tests_and_url_queues(dir_tree: dict) -> dict:
             project_path = os.path.join(page_folder_path, project)
             experiments_per_project[project] = {}
             for experiment in experiments:
-                url_queue = CustomEvaluationFramework.__get_url_queue(project, project_path, experiment)
-                experiments_per_project[project][experiment] = {
-                    'url_queue': url_queue,
-                    'runnable': CustomEvaluationFramework.is_runnable_experiment(project, experiment, dir_tree),
-                }
+                interaction_script = CustomEvaluationFramework.__get_interaction_script(project_path, experiment)
+                data = {}
+
+                if interaction_script is not None:
+                    data['interaction_script'] = interaction_script
+                else:
+                    url_queue = CustomEvaluationFramework.__get_url_queue(project, project_path, experiment)
+                    data['url_queue'] = url_queue
+
+                data['runnable'] = CustomEvaluationFramework.is_runnable_experiment(project, experiment, dir_tree)
+
+                experiments_per_project[project][experiment] = data
         return experiments_per_project
 
+    @staticmethod
+    def __get_interaction_script(project_path: str, experiment: str) -> list[str] | None:
+        interaction_file_path = os.path.join(project_path, experiment, 'interaction_script.cmd')
+        if os.path.isfile(interaction_file_path):
+            # If an interaction script is specified, it is parsed and used
+            with open(interaction_file_path) as file:
+                return file.readlines()
+        return None
+
     @staticmethod
     def __get_url_queue(project: str, project_path: str, experiment: str) -> list[str]:
         url_queue_file_path = os.path.join(project_path, experiment, 'url_queue.txt')
@@ -88,12 +105,18 @@ def perform_specific_evaluation(self, browser: Browser, params: TestParameters)
 
         is_dirty = False
         try:
-            url_queue = self.tests_per_project[params.evaluation_configuration.project][params.mech_group]['url_queue']
-            for url in url_queue:
-                tries = 0
-                while tries < 3:
-                    tries += 1
-                    browser.visit(url)
+            experiment = self.tests_per_project[params.evaluation_configuration.project][params.mech_group]
+
+            if 'interaction_script' in experiment:
+                interaction = Interaction(browser, experiment['interaction_script'])
+                interaction.execute()
+            else:
+                url_queue = experiment['url_queue']
+                for url in url_queue:
+                    tries = 0
+                    while tries < 3:
+                        tries += 1
+                        browser.visit(url)
         except Exception as e:
             logger.error(f'Error during test: {e}', exc_info=True)
             is_dirty = True
@@ -205,5 +228,5 @@ def include_file_headers(file_type: str) -> bool:
 
     def sync_with_folders(self):
         self.dir_tree = self.initialize_dir_tree()
-        self.tests_per_project = self.initialize_tests_and_url_queues(self.dir_tree)
+        self.tests_per_project = self.initialize_tests_and_interactions(self.dir_tree)
         logger.info('Framework is synced with folders')
diff --git a/experiments/pages/Support/UserInteraction/a.test/main/headers.json b/experiments/pages/Support/UserInteraction/a.test/main/headers.json
new file mode 100644
index 00000000..fe51488c
--- /dev/null
+++ b/experiments/pages/Support/UserInteraction/a.test/main/headers.json
@@ -0,0 +1 @@
+[]
diff --git a/experiments/pages/Support/UserInteraction/a.test/main/index.html b/experiments/pages/Support/UserInteraction/a.test/main/index.html
new file mode 100644
index 00000000..ad482c63
--- /dev/null
+++ b/experiments/pages/Support/UserInteraction/a.test/main/index.html
@@ -0,0 +1,6 @@
+<a href="http://a.test/report/?leak=UserInteraction" style="position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: red;" id="leak">
+    CLICK
+</a>
+<script>
+    document.getElementById('leak').click();
+</script>
\ No newline at end of file
diff --git a/experiments/pages/Support/UserInteraction/interaction_script.cmd b/experiments/pages/Support/UserInteraction/interaction_script.cmd
new file mode 100644
index 00000000..5daa56cf
--- /dev/null
+++ b/experiments/pages/Support/UserInteraction/interaction_script.cmd
@@ -0,0 +1 @@
+NAVIGATE https://a.test/Support/UserInteraction/main
diff --git a/requirements.in b/requirements.in
index b7055ad5..385a39ca 100644
--- a/requirements.in
+++ b/requirements.in
@@ -5,3 +5,4 @@ flatten-dict
 gunicorn
 pymongo
 requests
+websockets
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index d2968cc8..a5f13430 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
 #    pip-compile requirements.in
@@ -54,6 +54,8 @@ urllib3==2.2.3
     # via
     #   docker
     #   requests
+websockets==13.1
+    # via -r requirements.in
 werkzeug==3.0.4
     # via flask
 wsproto==1.2.0

From 5a516ba2765d2dc8bab09293163390ce1c3f8e93 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Wed, 30 Oct 2024 14:10:09 +0000
Subject: [PATCH 04/57] Connect browser interaction to terminal automation

---
 bci/browser/automation/terminal.py          | 35 +++++++++++++--------
 bci/browser/configuration/browser.py        | 21 ++++++++++---
 bci/browser/configuration/chromium.py       |  2 ++
 bci/browser/interaction/interaction.py      | 17 ++++++++--
 bci/evaluations/custom/custom_evaluation.py |  8 +++--
 5 files changed, 61 insertions(+), 22 deletions(-)

diff --git a/bci/browser/automation/terminal.py b/bci/browser/automation/terminal.py
index d1fe6f70..ed2235e1 100644
--- a/bci/browser/automation/terminal.py
+++ b/bci/browser/automation/terminal.py
@@ -7,22 +7,31 @@
 
 
 class TerminalAutomation:
-
     @staticmethod
-    def run(url: str, args: list[str], seconds_per_visit: int):
-        logger.debug("Starting browser process...")
+    def visit_url(url: str, args: list[str], seconds_per_visit: int):
         args.append(url)
+        proc, _ = TerminalAutomation.open_browser(args)
+        logger.debug(f'Visiting the page for {seconds_per_visit}s')
+        time.sleep(seconds_per_visit)
+        TerminalAutomation.terminate_browser(proc, args)
+
+    @staticmethod
+    def open_browser(args: list[str]) -> tuple[subprocess.Popen, str]:
+        logger.debug('Starting browser process...')
         logger.debug(f'Command string: \'{" ".join(args)}\'')
-        with open('/tmp/browser.log', 'a') as file:
-            proc = subprocess.Popen(
-                args,
-                stdout=file,
-                stderr=file
-            )
+        with open('/tmp/browser.log', 'a+') as file:
+            proc = subprocess.Popen(args, stdout=file, stderr=file)
+            time.sleep(0.5)
+            position = file.tell()
+            file.seek(0)
+            output = file.read()
+            file.seek(position)
+            return proc, output
 
-        time.sleep(seconds_per_visit)
+    @staticmethod
+    def terminate_browser(proc: subprocess.Popen, args: list[str]) -> None:
+        logger.debug('Terminating browser process using SIGINT...')
 
-        logger.debug(f'Terminating browser process after {seconds_per_visit}s using SIGINT...')
         # Use SIGINT and SIGTERM to end process such that cookies remain saved.
         proc.send_signal(signal.SIGINT)
         proc.send_signal(signal.SIGTERM)
@@ -30,8 +39,8 @@ def run(url: str, args: list[str], seconds_per_visit: int):
         try:
             stdout, stderr = proc.communicate(timeout=5)
         except subprocess.TimeoutExpired:
-            logger.info("Browser process did not terminate after 5s. Killing process through pkill...")
+            logger.info('Browser process did not terminate after 5s. Killing process through pkill...')
             subprocess.run(['pkill', '-2', args[0].split('/')[-1]])
 
         proc.wait()
-        logger.debug("Browser process terminated.")
+        logger.debug('Browser process terminated.')
diff --git a/bci/browser/configuration/browser.py b/bci/browser/configuration/browser.py
index 1178ece1..67419cd4 100644
--- a/bci/browser/configuration/browser.py
+++ b/bci/browser/configuration/browser.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+import subprocess
 from abc import abstractmethod
 
 import bci.browser.binary.factory as binary_factory
@@ -15,8 +16,11 @@
 
 
 class Browser:
+    process: subprocess.Popen
 
-    def __init__(self, browser_config: BrowserConfiguration, eval_config: EvaluationConfiguration, binary: Binary) -> None:
+    def __init__(
+        self, browser_config: BrowserConfiguration, eval_config: EvaluationConfiguration, binary: Binary
+    ) -> None:
         self.browser_config = browser_config
         self.eval_config = eval_config
         self.binary = binary
@@ -34,10 +38,17 @@ def visit(self, url: str):
         match self.eval_config.automation:
             case 'terminal':
                 args = self._get_terminal_args()
-                TerminalAutomation.run(url, args, self.eval_config.seconds_per_visit)
+                TerminalAutomation.visit_url(url, args, self.eval_config.seconds_per_visit)
             case _:
                 raise AttributeError('Not implemented')
 
+    def open(self) -> str:
+        self.process, output = TerminalAutomation.open_browser(self._get_terminal_args())
+        return output
+
+    def terminate(self):
+        TerminalAutomation.terminate_browser(self.process, self._get_terminal_args())
+
     def pre_evaluation_setup(self):
         self.__fetch_binary()
 
@@ -80,11 +91,13 @@ def _get_executable_file_path(self) -> str:
         return os.path.join(self.__get_execution_folder_path(), self.binary.executable_name)
 
     @abstractmethod
-    def _get_terminal_args(self):
+    def _get_terminal_args(self) -> list[str]:
         pass
 
     @staticmethod
-    def get_browser(browser_config: BrowserConfiguration, eval_config: EvaluationConfiguration, state: State) -> Browser:
+    def get_browser(
+        browser_config: BrowserConfiguration, eval_config: EvaluationConfiguration, state: State
+    ) -> Browser:
         from bci.browser.configuration.chromium import Chromium
         from bci.browser.configuration.firefox import Firefox
 
diff --git a/bci/browser/configuration/chromium.py b/bci/browser/configuration/chromium.py
index 6108328d..3aa0f8e3 100644
--- a/bci/browser/configuration/chromium.py
+++ b/bci/browser/configuration/chromium.py
@@ -1,6 +1,7 @@
 from bci.browser.configuration.browser import Browser
 from bci.browser.configuration.options import Default, BlockThirdPartyCookies, PrivateBrowsing
 from bci.browser.configuration.profile import prepare_chromium_profile
+from bci.browser.interaction.interaction import Interaction
 
 SUPPORTED_OPTIONS = [
     Default(),
@@ -41,6 +42,7 @@ def _get_terminal_args(self) -> list[str]:
         args.append('--enable-logging')
         args.append('--v=1')
         args.append('--log-level=0')
+        args.append(f'--remote-debugging-port={Interaction.port}')
         # Headless changed from version +/- 110 onwards: https://developer.chrome.com/docs/chromium/new-headless
         # Using the `--headless` flag will crash the browser for these later versions.
         # Also see: https://github.com/DistriNet/BugHog/issues/12
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index 8a014ac1..1f867a0a 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -1,13 +1,24 @@
+from bci.browser.automation.terminal import TerminalAutomation
 from bci.browser.configuration.browser import Browser as BrowserConfig
 
 
 class Interaction:
-    browser_config: BrowserConfig
+    port = 9222
+
+    browser: BrowserConfig
     script: list[str]
 
     def __init__(self, browser: BrowserConfig, script: list[str]) -> None:
-        self.browser_config = browser
+        self.browser = browser
         self.script = script
 
     def execute(self) -> None:
-        print(f'TODO - execute {self.browser_config._get_terminal_args()} with script {", ".join(self.script)}')
+        output = self.browser.open()
+
+        # TODO - identify browser from the output
+        # TODO - initialize the browser
+        # TODO - parse the script and run the commands
+        # TODO - visit the sanity check URL
+        # TODO - destroy the browser
+
+        self.browser.terminate()
diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index 3f235378..b2d97ef3 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -107,14 +107,18 @@ def perform_specific_evaluation(self, browser: Browser, params: TestParameters)
         try:
             experiment = self.tests_per_project[params.evaluation_configuration.project][params.mech_group]
 
+            max_tries = 3
             if 'interaction_script' in experiment:
                 interaction = Interaction(browser, experiment['interaction_script'])
-                interaction.execute()
+                tries = 0
+                while tries < max_tries:
+                    tries += 1
+                    interaction.execute()
             else:
                 url_queue = experiment['url_queue']
                 for url in url_queue:
                     tries = 0
-                    while tries < 3:
+                    while tries < max_tries:
                         tries += 1
                         browser.visit(url)
         except Exception as e:

From 6cef7597894fef52a5236a8e5521440453b855ff Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Wed, 30 Oct 2024 14:26:05 +0000
Subject: [PATCH 05/57] Install pip requirements in dev container

---
 .devcontainer/devcontainer.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 8687890c..16cc9c75 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -24,7 +24,10 @@
 				"Vue.volar"
 			]
 		}
-	}
+	},
+
+	// Install pip requirements
+	"postCreateCommand": "pip install -r requirements.txt"
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -35,9 +38,6 @@
 	// Uncomment the next line if you want to keep your containers running after VS Code shuts down.
 	// "shutdownAction": "none",
 
-	// Uncomment the next line to run commands after the container is created.
-	// "postCreateCommand": "cat /etc/os-release",
-
 	// Configure tool-specific properties.
 	// "customizations": {},
 }

From 688948fcb7748dd5011c355b1c6e716043a0f56d Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Wed, 30 Oct 2024 14:43:36 +0000
Subject: [PATCH 06/57] Simple interaction browser identification

---
 bci/browser/interaction/browsers/chromium.py |  2 +-
 bci/browser/interaction/interaction.py       | 25 +++++++++++++++-----
 2 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/bci/browser/interaction/browsers/chromium.py b/bci/browser/interaction/browsers/chromium.py
index b82c7014..7db878af 100644
--- a/bci/browser/interaction/browsers/chromium.py
+++ b/bci/browser/interaction/browsers/chromium.py
@@ -31,7 +31,7 @@ def close_connection(self):
 
     def navigate(self, url):
         self.send({'sessionId': self.session_id, 'method': 'Page.navigate', 'params': {'url': url}})
-        sleep(0.01)
+        sleep(0.5)
 
     def click(self, x, y):
         self.send(
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index 1f867a0a..518d5ee4 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -1,5 +1,8 @@
-from bci.browser.automation.terminal import TerminalAutomation
+import re
+
 from bci.browser.configuration.browser import Browser as BrowserConfig
+from bci.browser.interaction.browsers.browser import Browser
+from bci.browser.interaction.browsers.chromium import Chromium
 
 
 class Interaction:
@@ -15,10 +18,20 @@ def __init__(self, browser: BrowserConfig, script: list[str]) -> None:
     def execute(self) -> None:
         output = self.browser.open()
 
-        # TODO - identify browser from the output
-        # TODO - initialize the browser
-        # TODO - parse the script and run the commands
-        # TODO - visit the sanity check URL
-        # TODO - destroy the browser
+        interaction_browser = self._initiate_browser(output)
+
+        # TODO - parse the script and run the commands instead
+        interaction_browser.navigate('https://a.test/Support/UserInteraction/main')
+
+        interaction_browser.navigate('https://a.test/report/?bughog_sanity_check=OK')
+        interaction_browser.close_connection()
 
         self.browser.terminate()
+
+    def _initiate_browser(self, init_output: str) -> Browser:
+        cdp = re.search(r'DevTools listening on ws:\/\/127\.0\.0\.1:9222\/devtools\/browser\/(.+)\n', init_output)
+
+        if cdp:
+            return Chromium(browser_id=cdp.group(1), port=Interaction.port)
+
+        raise Exception('Unrecognized browser')

From b2f1f828e1bbb3b9615b659787f10f8e7bd35661 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Wed, 30 Oct 2024 14:48:26 +0000
Subject: [PATCH 07/57] Fix browser log reading

---
 bci/browser/automation/terminal.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/bci/browser/automation/terminal.py b/bci/browser/automation/terminal.py
index ed2235e1..77869206 100644
--- a/bci/browser/automation/terminal.py
+++ b/bci/browser/automation/terminal.py
@@ -20,12 +20,13 @@ def open_browser(args: list[str]) -> tuple[subprocess.Popen, str]:
         logger.debug('Starting browser process...')
         logger.debug(f'Command string: \'{" ".join(args)}\'')
         with open('/tmp/browser.log', 'a+') as file:
+            initial_position = file.tell()
             proc = subprocess.Popen(args, stdout=file, stderr=file)
             time.sleep(0.5)
-            position = file.tell()
-            file.seek(0)
+            last_position = file.tell()
+            file.seek(initial_position)
             output = file.read()
-            file.seek(position)
+            file.seek(last_position)
             return proc, output
 
     @staticmethod

From e8f56a2903c5868ae76ce12ed82b28476ed91743 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Wed, 30 Oct 2024 15:19:17 +0000
Subject: [PATCH 08/57] Browser interaction commands interpreter

---
 bci/browser/interaction/browsers/browser.py |  2 ++
 bci/browser/interaction/interaction.py      | 28 +++++++++++++++++++--
 2 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/bci/browser/interaction/browsers/browser.py b/bci/browser/interaction/browsers/browser.py
index a969fcce..fcee439b 100644
--- a/bci/browser/interaction/browsers/browser.py
+++ b/bci/browser/interaction/browsers/browser.py
@@ -28,6 +28,8 @@ class Browser(ABC):
     ws_timeout: float
     ws: ClientConnection
 
+    public_methods: list[str] = ['navigate', 'click']
+
     def __init__(self, browser_id: str = '', port: int = 9222, host: str = '127.0.0.1', autoclose_timeout: float = 0.5):
         self.ws_timeout = autoclose_timeout
         self.ws = connect(self.get_ws_endpoint(host, port, browser_id), close_timeout=autoclose_timeout)
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index 518d5ee4..65b582b0 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -1,9 +1,13 @@
+import logging
 import re
+from inspect import signature
 
 from bci.browser.configuration.browser import Browser as BrowserConfig
 from bci.browser.interaction.browsers.browser import Browser
 from bci.browser.interaction.browsers.chromium import Chromium
 
+logger = logging.getLogger(__name__)
+
 
 class Interaction:
     port = 9222
@@ -20,8 +24,7 @@ def execute(self) -> None:
 
         interaction_browser = self._initiate_browser(output)
 
-        # TODO - parse the script and run the commands instead
-        interaction_browser.navigate('https://a.test/Support/UserInteraction/main')
+        self._interpret(interaction_browser)
 
         interaction_browser.navigate('https://a.test/report/?bughog_sanity_check=OK')
         interaction_browser.close_connection()
@@ -35,3 +38,24 @@ def _initiate_browser(self, init_output: str) -> Browser:
             return Chromium(browser_id=cdp.group(1), port=Interaction.port)
 
         raise Exception('Unrecognized browser')
+
+    def _interpret(self, browser: Browser) -> None:
+        for statement in self.script:
+            cmd, *args = statement.split()
+            method_name = cmd.lower()
+
+            if method_name not in Browser.public_methods:
+                raise Exception(
+                    f'Invalid command `{cmd}`. Expected one of {", ".join(map(lambda m: m.upper(), Browser.public_methods))}.'
+                )
+
+            method = getattr(browser, method_name)
+            method_params_len = len(signature(method).parameters)
+
+            if method_params_len != len(args):
+                raise Exception(
+                    f'Invalid number of arguments for command `{cmd}`. Expected {method_params_len}, got {len(args)}.'
+                )
+
+            logger.debug(f'Executing interaction method `{method_name}` with the arguments {args}')
+            method(*args)

From c0e47903e97a42eded3617864d2166275d7af134 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Wed, 30 Oct 2024 16:55:44 +0000
Subject: [PATCH 09/57] Basic BiDi implementation

---
 bci/browser/configuration/chromium.py       |  3 +--
 bci/browser/configuration/firefox.py        |  4 ++--
 bci/browser/interaction/browsers/browser.py |  2 +-
 bci/browser/interaction/browsers/firefox.py | 11 ++++++-----
 bci/browser/interaction/interaction.py      | 20 ++++++++++++++++----
 5 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/bci/browser/configuration/chromium.py b/bci/browser/configuration/chromium.py
index 3aa0f8e3..c2d70ea4 100644
--- a/bci/browser/configuration/chromium.py
+++ b/bci/browser/configuration/chromium.py
@@ -1,7 +1,6 @@
 from bci.browser.configuration.browser import Browser
 from bci.browser.configuration.options import Default, BlockThirdPartyCookies, PrivateBrowsing
 from bci.browser.configuration.profile import prepare_chromium_profile
-from bci.browser.interaction.interaction import Interaction
 
 SUPPORTED_OPTIONS = [
     Default(),
@@ -42,7 +41,7 @@ def _get_terminal_args(self) -> list[str]:
         args.append('--enable-logging')
         args.append('--v=1')
         args.append('--log-level=0')
-        args.append(f'--remote-debugging-port={Interaction.port}')
+        args.append('--remote-debugging-port=0')
         # Headless changed from version +/- 110 onwards: https://developer.chrome.com/docs/chromium/new-headless
         # Using the `--headless` flag will crash the browser for these later versions.
         # Also see: https://github.com/DistriNet/BugHog/issues/12
diff --git a/bci/browser/configuration/firefox.py b/bci/browser/configuration/firefox.py
index 643ae57c..c6918d70 100644
--- a/bci/browser/configuration/firefox.py
+++ b/bci/browser/configuration/firefox.py
@@ -2,10 +2,9 @@
 
 from bci import cli
 from bci.browser.configuration.browser import Browser
-from bci.browser.configuration.options import Default, BlockThirdPartyCookies, PrivateBrowsing, TrackingProtection
+from bci.browser.configuration.options import BlockThirdPartyCookies, Default, PrivateBrowsing, TrackingProtection
 from bci.browser.configuration.profile import prepare_firefox_profile
 
-
 SUPPORTED_OPTIONS = [
     Default(),
     BlockThirdPartyCookies(),
@@ -26,6 +25,7 @@ def _get_terminal_args(self) -> list[str]:
 
         args = [self._get_executable_file_path()]
         args.extend(['-profile', self._profile_path])
+        args.append('--remote-debugging-port=0')
         user_prefs = []
 
         def add_user_pref(key: str, value: str | int | bool):
diff --git a/bci/browser/interaction/browsers/browser.py b/bci/browser/interaction/browsers/browser.py
index fcee439b..94dcc5ff 100644
--- a/bci/browser/interaction/browsers/browser.py
+++ b/bci/browser/interaction/browsers/browser.py
@@ -30,7 +30,7 @@ class Browser(ABC):
 
     public_methods: list[str] = ['navigate', 'click']
 
-    def __init__(self, browser_id: str = '', port: int = 9222, host: str = '127.0.0.1', autoclose_timeout: float = 0.5):
+    def __init__(self, browser_id: str = '', port: int = 9222, host: str = '127.0.0.1', autoclose_timeout: float = 2):
         self.ws_timeout = autoclose_timeout
         self.ws = connect(self.get_ws_endpoint(host, port, browser_id), close_timeout=autoclose_timeout)
         self.initialize_connection(browser_id, port, host)
diff --git a/bci/browser/interaction/browsers/firefox.py b/bci/browser/interaction/browsers/firefox.py
index 97dd7202..9f5d6f02 100644
--- a/bci/browser/interaction/browsers/firefox.py
+++ b/bci/browser/interaction/browsers/firefox.py
@@ -46,11 +46,12 @@ def navigate(self, url):
         # Wait for the DOM to load
         self.listen(
             'browsingContext.domContentLoaded',
-            {
-                'url': url,
-                'context': self.browsing_context,
-                'navigation': navigation,
-            },
+            {}
+            #{
+            #    'url': url,
+            #    'context': self.browsing_context,
+            #    'navigation': navigation,
+            #},
         )
 
     def click(self, x, y):
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index 65b582b0..a3c98488 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -5,13 +5,12 @@
 from bci.browser.configuration.browser import Browser as BrowserConfig
 from bci.browser.interaction.browsers.browser import Browser
 from bci.browser.interaction.browsers.chromium import Chromium
+from bci.browser.interaction.browsers.firefox import Firefox
 
 logger = logging.getLogger(__name__)
 
 
 class Interaction:
-    port = 9222
-
     browser: BrowserConfig
     script: list[str]
 
@@ -32,10 +31,23 @@ def execute(self) -> None:
         self.browser.terminate()
 
     def _initiate_browser(self, init_output: str) -> Browser:
-        cdp = re.search(r'DevTools listening on ws:\/\/127\.0\.0\.1:9222\/devtools\/browser\/(.+)\n', init_output)
+        print(init_output)
+
+        cdp = re.search(
+            r'DevTools listening on ws:\/\/(.+):(.+)\/devtools\/browser\/(.+)\n',
+            init_output,
+        )
 
         if cdp:
-            return Chromium(browser_id=cdp.group(1), port=Interaction.port)
+            return Chromium(browser_id=cdp.group(3), port=int(cdp.group(2)), host=cdp.group(1))
+
+        bidi = re.search(
+            r'WebDriver BiDi listening on ws:\/\/(.+):(.+)',
+            init_output,
+        )
+
+        if bidi:
+            return Firefox(port=int(bidi.group(2)), host=bidi.group(1))
 
         raise Exception('Unrecognized browser')
 

From 796bf93e22007beaeeae4b518270f19f6e418a22 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Wed, 30 Oct 2024 16:57:12 +0000
Subject: [PATCH 10/57] Remove print

---
 bci/browser/interaction/interaction.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index a3c98488..f0186382 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -31,8 +31,6 @@ def execute(self) -> None:
         self.browser.terminate()
 
     def _initiate_browser(self, init_output: str) -> Browser:
-        print(init_output)
-
         cdp = re.search(
             r'DevTools listening on ws:\/\/(.+):(.+)\/devtools\/browser\/(.+)\n',
             init_output,

From c2c5580561c09294f6082897c3984f74a66c9e6e Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 08:55:56 +0000
Subject: [PATCH 11/57] Simple AutoGUI test experiment

---
 experiments/pages/Support/AutoGUI/a.test/main/headers.json | 1 +
 experiments/pages/Support/AutoGUI/a.test/main/index.html   | 1 +
 experiments/pages/Support/AutoGUI/interaction_script.cmd   | 2 ++
 3 files changed, 4 insertions(+)
 create mode 100644 experiments/pages/Support/AutoGUI/a.test/main/headers.json
 create mode 100644 experiments/pages/Support/AutoGUI/a.test/main/index.html
 create mode 100644 experiments/pages/Support/AutoGUI/interaction_script.cmd

diff --git a/experiments/pages/Support/AutoGUI/a.test/main/headers.json b/experiments/pages/Support/AutoGUI/a.test/main/headers.json
new file mode 100644
index 00000000..fe51488c
--- /dev/null
+++ b/experiments/pages/Support/AutoGUI/a.test/main/headers.json
@@ -0,0 +1 @@
+[]
diff --git a/experiments/pages/Support/AutoGUI/a.test/main/index.html b/experiments/pages/Support/AutoGUI/a.test/main/index.html
new file mode 100644
index 00000000..4c9318e8
--- /dev/null
+++ b/experiments/pages/Support/AutoGUI/a.test/main/index.html
@@ -0,0 +1 @@
+<a href="https://a.test/report/?leak=AutoGUI" style="position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: red;">CLICK</a>
\ No newline at end of file
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/interaction_script.cmd
new file mode 100644
index 00000000..92690174
--- /dev/null
+++ b/experiments/pages/Support/AutoGUI/interaction_script.cmd
@@ -0,0 +1,2 @@
+NAVIGATE https://a.test/Support/AutoGUI/main
+CLICK 100 100
\ No newline at end of file

From b8c02dd5be326749c7cadd03504887dd61f28181 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 09:01:13 +0000
Subject: [PATCH 12/57] Install AutoGUI

---
 requirements.in  |  3 ++-
 requirements.txt | 20 ++++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/requirements.in b/requirements.in
index 385a39ca..814ea5bf 100644
--- a/requirements.in
+++ b/requirements.in
@@ -5,4 +5,5 @@ flatten-dict
 gunicorn
 pymongo
 requests
-websockets
\ No newline at end of file
+websockets
+pyautogui
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index a5f13430..c03e9c00 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -38,10 +38,30 @@ markupsafe==3.0.2
     # via
     #   jinja2
     #   werkzeug
+mouseinfo==0.1.3
+    # via pyautogui
 packaging==24.1
     # via gunicorn
+pyautogui==0.9.54
+    # via -r requirements.in
+pygetwindow==0.0.9
+    # via pyautogui
 pymongo==4.10.1
     # via -r requirements.in
+pymsgbox==1.0.9
+    # via pyautogui
+pyperclip==1.9.0
+    # via mouseinfo
+pyrect==0.2.0
+    # via pygetwindow
+pyscreeze==1.0.1
+    # via pyautogui
+python3-xlib==0.15
+    # via
+    #   mouseinfo
+    #   pyautogui
+pytweening==1.2.0
+    # via pyautogui
 requests==2.32.3
     # via
     #   -r requirements.in

From 1444ff2de22fbede606e9c9f3ea64b00c924c1b0 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 10:07:16 +0000
Subject: [PATCH 13/57] Simple AutoGUI usage

---
 Dockerfile                                  |   4 +
 bci/browser/configuration/browser.py        |  13 ++-
 bci/browser/interaction/browsers/browser.py | 106 +++++++-------------
 bci/browser/interaction/interaction.py      |  13 ++-
 requirements.in                             |   6 +-
 requirements.txt                            |  12 ++-
 6 files changed, 67 insertions(+), 87 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index b7bd1020..9439b3d8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -54,7 +54,11 @@ RUN cp /app/scripts/daemon/xvfb /etc/init.d/xvfb
 # Install python packages
 COPY requirements.txt /app/requirements.txt
 RUN pip install --user -r /app/requirements.txt
+RUN apt-get install python3-tk python3-xlib gnome-screenshot -y
 
+# Initiate PyAutoGUI
+RUN touch /root/.Xauthority && \
+    xauth add ${HOST}:0 . $(xxd -l 16 -p /dev/urandom)
 
 FROM base AS core
 # Copy rest of source code
diff --git a/bci/browser/configuration/browser.py b/bci/browser/configuration/browser.py
index 67419cd4..707f53d3 100644
--- a/bci/browser/configuration/browser.py
+++ b/bci/browser/configuration/browser.py
@@ -16,12 +16,13 @@
 
 
 class Browser:
-    process: subprocess.Popen
+    process: subprocess.Popen | None
 
     def __init__(
         self, browser_config: BrowserConfiguration, eval_config: EvaluationConfiguration, binary: Binary
     ) -> None:
         self.browser_config = browser_config
+        self.process = None
         self.eval_config = eval_config
         self.binary = binary
         self.state = binary.state
@@ -42,12 +43,18 @@ def visit(self, url: str):
             case _:
                 raise AttributeError('Not implemented')
 
-    def open(self) -> str:
-        self.process, output = TerminalAutomation.open_browser(self._get_terminal_args())
+    def open(self, url: str) -> str:
+        args = self._get_terminal_args()
+        args.append(url)
+        self.process, output = TerminalAutomation.open_browser(args)
         return output
 
     def terminate(self):
+        if self.process is None:
+            return
+
         TerminalAutomation.terminate_browser(self.process, self._get_terminal_args())
+        self.process = None
 
     def pre_evaluation_setup(self):
         self.__fetch_binary()
diff --git a/bci/browser/interaction/browsers/browser.py b/bci/browser/interaction/browsers/browser.py
index 94dcc5ff..cdfec4ae 100644
--- a/bci/browser/interaction/browsers/browser.py
+++ b/bci/browser/interaction/browsers/browser.py
@@ -1,84 +1,46 @@
-import json
-from abc import ABC, abstractmethod
+import base64
+import os
+from io import BytesIO
+from time import sleep
 
-from websockets.sync.client import ClientConnection, connect
+import pyautogui as gui
+import Xlib.display
+from pyvirtualdisplay.display import Display
 
+from bci.browser.configuration.browser import Browser as BrowserConfig
 
-# Returns true if:
-# - required == True -> all fields from `pattern` are present in `data` with the same value
-# - required == False -> all fields from `pattern` which are present in `data` have the same value
-def dictionaries_match(pattern: dict, data: dict, required: bool) -> bool:
-    for key in pattern:
-        if required and key not in data:
-            return False
-
-        if key in data:
-            # Equal values, up to slashes
-            if (
-                not dictionaries_match(pattern[key], data[key], required)
-                if isinstance(pattern[key], dict)
-                else str(data[key]).replace('/', '') != str(pattern[key]).replace('/', '')
-            ):
-                return False
-    return True
-
-
-class Browser(ABC):
-    request_id: int = 0
-    ws_timeout: float
-    ws: ClientConnection
 
+class Browser:
+    browser_config: BrowserConfig
     public_methods: list[str] = ['navigate', 'click']
 
-    def __init__(self, browser_id: str = '', port: int = 9222, host: str = '127.0.0.1', autoclose_timeout: float = 2):
-        self.ws_timeout = autoclose_timeout
-        self.ws = connect(self.get_ws_endpoint(host, port, browser_id), close_timeout=autoclose_timeout)
-        self.initialize_connection(browser_id, port, host)
-
-    def req_id(self) -> int:
-        self.request_id += 1
-        return self.request_id
-
-    def send(self, data: dict) -> dict:
-        data['id'] = self.req_id()
-
-        self.ws.send(json.dumps(data))
-
-        return self.receive({'method': data['method'], 'id': data['id']}, False)
-
-    def listen(self, event: str, params: dict) -> dict:
-        return self.receive({'type': 'event', 'method': event, 'params': params}, True)
-
-    def receive(self, data: dict, required: bool) -> dict:
-        result = None
-
-        while result == None or (not dictionaries_match(data, result, required)):
-            result = json.loads(self.ws.recv(self.ws_timeout))
-
-            if 'type' in result and result['type'] == 'error':
-                raise Exception(f'Received browser error: {result}')
+    def __init__(self, browser_config: BrowserConfig):
+        self.browser_config = browser_config
+        disp = Display(visible=True, size=(1920, 1080), backend='xvfb', use_xauth=True)
+        disp.start()
+        gui._pyautogui_x11._display = Xlib.display.Display(os.environ['DISPLAY'])
 
-        return result
+    def __del__(self):
+        self.browser_config.terminate()
 
-    # --- BROWSER-SPECIFIC METHODS ---
-    @abstractmethod
-    def get_ws_endpoint(self, host: str, port: int, browser_id: str) -> str:
-        pass
+    # --- PUBLIC METHODS ---
+    def navigate(self, url: str):
+        self.browser_config.terminate()
+        self.browser_config.open(url)
 
-    @abstractmethod
-    def initialize_connection(self, _browserId, _port, _host):
-        pass
+        # TODO - convert this into an argument or a separate command
+        sleep(0.5)
 
-    @abstractmethod
-    def close_connection(
-        self,
-    ):
-        pass
+    def click(self, x: str, y: str):
+        # print(gui.size())
+        # print(gui.position())
+        # gui.moveTo(int(x), int(y))
+        gui.moveTo(100, 540)
+        gui.click()
 
-    @abstractmethod
-    def navigate(self, _url):
-        pass
+        # buffered = BytesIO()
+        # print(gui.screenshot().save(buffered, format='JPEG'))
+        # img_str = base64.b64encode(buffered.getvalue())
+        # print(img_str.decode('utf-8'))
 
-    @abstractmethod
-    def click(self, _x, _y):
-        pass
+        sleep(0.5)
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index f0186382..e84c4328 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -19,18 +19,16 @@ def __init__(self, browser: BrowserConfig, script: list[str]) -> None:
         self.script = script
 
     def execute(self) -> None:
-        output = self.browser.open()
-
-        interaction_browser = self._initiate_browser(output)
+        interaction_browser = self._initiate_browser()
 
         self._interpret(interaction_browser)
 
         interaction_browser.navigate('https://a.test/report/?bughog_sanity_check=OK')
-        interaction_browser.close_connection()
-
-        self.browser.terminate()
 
-    def _initiate_browser(self, init_output: str) -> Browser:
+    def _initiate_browser(self) -> Browser:
+        # TODO - possibly return different browser instances
+        return Browser(self.browser)
+        """
         cdp = re.search(
             r'DevTools listening on ws:\/\/(.+):(.+)\/devtools\/browser\/(.+)\n',
             init_output,
@@ -48,6 +46,7 @@ def _initiate_browser(self, init_output: str) -> Browser:
             return Firefox(port=int(bidi.group(2)), host=bidi.group(1))
 
         raise Exception('Unrecognized browser')
+        """
 
     def _interpret(self, browser: Browser) -> None:
         for statement in self.script:
diff --git a/requirements.in b/requirements.in
index 814ea5bf..f0993275 100644
--- a/requirements.in
+++ b/requirements.in
@@ -5,5 +5,7 @@ flatten-dict
 gunicorn
 pymongo
 requests
-websockets
-pyautogui
\ No newline at end of file
+pyautogui
+pyvirtualdisplay
+Pillow
+Xlib
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index c03e9c00..2a367b96 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -42,6 +42,8 @@ mouseinfo==0.1.3
     # via pyautogui
 packaging==24.1
     # via gunicorn
+pillow==11.0.0
+    # via -r requirements.in
 pyautogui==0.9.54
     # via -r requirements.in
 pygetwindow==0.0.9
@@ -62,6 +64,8 @@ python3-xlib==0.15
     #   pyautogui
 pytweening==1.2.0
     # via pyautogui
+pyvirtualdisplay==3.0
+    # via -r requirements.in
 requests==2.32.3
     # via
     #   -r requirements.in
@@ -69,14 +73,16 @@ requests==2.32.3
 simple-websocket==1.1.0
     # via flask-sock
 six==1.16.0
-    # via flatten-dict
+    # via
+    #   flatten-dict
+    #   xlib
 urllib3==2.2.3
     # via
     #   docker
     #   requests
-websockets==13.1
-    # via -r requirements.in
 werkzeug==3.0.4
     # via flask
 wsproto==1.2.0
     # via simple-websocket
+xlib==0.21
+    # via -r requirements.in

From 0acc9c204d9cba8d7862167f7139b9a63be516a4 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 10:17:02 +0000
Subject: [PATCH 14/57] Remove debugging ports

---
 bci/browser/configuration/chromium.py | 1 -
 bci/browser/configuration/firefox.py  | 1 -
 2 files changed, 2 deletions(-)

diff --git a/bci/browser/configuration/chromium.py b/bci/browser/configuration/chromium.py
index c2d70ea4..6108328d 100644
--- a/bci/browser/configuration/chromium.py
+++ b/bci/browser/configuration/chromium.py
@@ -41,7 +41,6 @@ def _get_terminal_args(self) -> list[str]:
         args.append('--enable-logging')
         args.append('--v=1')
         args.append('--log-level=0')
-        args.append('--remote-debugging-port=0')
         # Headless changed from version +/- 110 onwards: https://developer.chrome.com/docs/chromium/new-headless
         # Using the `--headless` flag will crash the browser for these later versions.
         # Also see: https://github.com/DistriNet/BugHog/issues/12
diff --git a/bci/browser/configuration/firefox.py b/bci/browser/configuration/firefox.py
index c6918d70..c336190b 100644
--- a/bci/browser/configuration/firefox.py
+++ b/bci/browser/configuration/firefox.py
@@ -25,7 +25,6 @@ def _get_terminal_args(self) -> list[str]:
 
         args = [self._get_executable_file_path()]
         args.extend(['-profile', self._profile_path])
-        args.append('--remote-debugging-port=0')
         user_prefs = []
 
         def add_user_pref(key: str, value: str | int | bool):

From 840190a8cdd5447039e4c732e32548cae0ffb83d Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 11:14:46 +0000
Subject: [PATCH 15/57] Fix opening Firefox

---
 bci/browser/automation/terminal.py   | 12 +++---------
 bci/browser/configuration/browser.py |  5 ++---
 2 files changed, 5 insertions(+), 12 deletions(-)

diff --git a/bci/browser/automation/terminal.py b/bci/browser/automation/terminal.py
index 77869206..ddc08b8e 100644
--- a/bci/browser/automation/terminal.py
+++ b/bci/browser/automation/terminal.py
@@ -10,24 +10,18 @@ class TerminalAutomation:
     @staticmethod
     def visit_url(url: str, args: list[str], seconds_per_visit: int):
         args.append(url)
-        proc, _ = TerminalAutomation.open_browser(args)
+        proc = TerminalAutomation.open_browser(args)
         logger.debug(f'Visiting the page for {seconds_per_visit}s')
         time.sleep(seconds_per_visit)
         TerminalAutomation.terminate_browser(proc, args)
 
     @staticmethod
-    def open_browser(args: list[str]) -> tuple[subprocess.Popen, str]:
+    def open_browser(args: list[str]) -> subprocess.Popen:
         logger.debug('Starting browser process...')
         logger.debug(f'Command string: \'{" ".join(args)}\'')
         with open('/tmp/browser.log', 'a+') as file:
-            initial_position = file.tell()
             proc = subprocess.Popen(args, stdout=file, stderr=file)
-            time.sleep(0.5)
-            last_position = file.tell()
-            file.seek(initial_position)
-            output = file.read()
-            file.seek(last_position)
-            return proc, output
+            return proc
 
     @staticmethod
     def terminate_browser(proc: subprocess.Popen, args: list[str]) -> None:
diff --git a/bci/browser/configuration/browser.py b/bci/browser/configuration/browser.py
index 707f53d3..0247f28e 100644
--- a/bci/browser/configuration/browser.py
+++ b/bci/browser/configuration/browser.py
@@ -43,11 +43,10 @@ def visit(self, url: str):
             case _:
                 raise AttributeError('Not implemented')
 
-    def open(self, url: str) -> str:
+    def open(self, url: str) -> None:
         args = self._get_terminal_args()
         args.append(url)
-        self.process, output = TerminalAutomation.open_browser(args)
-        return output
+        self.process = TerminalAutomation.open_browser(args)
 
     def terminate(self):
         if self.process is None:

From c85fa2a198af6a45748fbad00606ed692da4e59d Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 11:15:15 +0000
Subject: [PATCH 16/57] Fix opening Firefox

---
 bci/browser/configuration/firefox.py        | 2 ++
 bci/browser/interaction/browsers/browser.py | 3 ++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/bci/browser/configuration/firefox.py b/bci/browser/configuration/firefox.py
index c336190b..4310bf20 100644
--- a/bci/browser/configuration/firefox.py
+++ b/bci/browser/configuration/firefox.py
@@ -25,6 +25,7 @@ def _get_terminal_args(self) -> list[str]:
 
         args = [self._get_executable_file_path()]
         args.extend(['-profile', self._profile_path])
+        args.append('-setDefaultBrowser')
         user_prefs = []
 
         def add_user_pref(key: str, value: str | int | bool):
@@ -44,6 +45,7 @@ def add_user_pref(key: str, value: str | int | bool):
         # add_user_pref('network.proxy.type', 1)
 
         add_user_pref('app.update.enabled', False)
+        add_user_pref('browser.shell.checkDefaultBrowser', False)
         if 'default' in self.browser_config.browser_setting:
             pass
         elif 'btpc' in self.browser_config.browser_setting:
diff --git a/bci/browser/interaction/browsers/browser.py b/bci/browser/interaction/browsers/browser.py
index cdfec4ae..2d45dafd 100644
--- a/bci/browser/interaction/browsers/browser.py
+++ b/bci/browser/interaction/browsers/browser.py
@@ -29,12 +29,13 @@ def navigate(self, url: str):
         self.browser_config.open(url)
 
         # TODO - convert this into an argument or a separate command
-        sleep(0.5)
+        sleep(2)
 
     def click(self, x: str, y: str):
         # print(gui.size())
         # print(gui.position())
         # gui.moveTo(int(x), int(y))
+
         gui.moveTo(100, 540)
         gui.click()
 

From e7cfbd94e5320788f89cf277a4dc882636db75bb Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Thu, 31 Oct 2024 11:18:28 +0000
Subject: [PATCH 17/57] Improve PoC editor

- Change internal tree representation for experiments
- Store python backend logic as files without folder
- Existing url_queue.txt files can be editor through web UI
---
 bci/evaluations/custom/custom_evaluation.py   | 41 ++++++---
 bci/web/blueprints/api.py                     | 78 +++++++++++-----
 bci/web/blueprints/experiments.py             | 68 +++++++-------
 bci/web/vue/src/components/poc-editor.vue     | 90 ++++++++++++++-----
 .../a.test/{py-server/index.py => server.py}  |  2 +-
 nginx/config/experiments.conf                 | 51 +++++------
 6 files changed, 215 insertions(+), 115 deletions(-)
 rename experiments/pages/Support/PythonServer/a.test/{py-server/index.py => server.py} (98%)

diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index 279065e3..66130646 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -20,19 +20,29 @@ def __init__(self):
 
     @staticmethod
     def initialize_dir_tree() -> dict:
+        """
+        Initializes directory tree of experiments.
+        """
         path = Global.custom_page_folder
-
-        def path_to_dict(path):
-            if os.path.isdir(path):
-                return {
-                    sub_folder: path_to_dict(os.path.join(path, sub_folder))
-                    for sub_folder in os.listdir(path)
-                    if sub_folder != 'url_queue.txt'
-                }
+        dir_tree = {}
+
+        def set_nested_value(d: dict, keys: list[str], value: dict):
+            nested_dict = d
+            for key in keys[:-1]:
+                nested_dict = nested_dict[key]
+            nested_dict[keys[-1]] = value
+
+        for root, dirs, files in os.walk(path):
+            # Remove base path from root
+            root = root[len(path):]
+            keys = root.split('/')[1:]
+            subdir_tree = {dir: {} for dir in dirs} | {file: None for file in files}
+            if root:
+                set_nested_value(dir_tree, keys, subdir_tree)
             else:
-                return os.path.basename(path)
+                dir_tree = subdir_tree
 
-        return path_to_dict(path)
+        return dir_tree
 
     @staticmethod
     def initialize_tests_and_url_queues(dir_tree: dict) -> dict:
@@ -70,11 +80,14 @@ def __get_url_queue(project: str, project_path: str, experiment: str) -> list[st
         raise AttributeError(f"Could not infer url queue for experiment '{experiment}' in project '{project}'")
 
     @staticmethod
-    def is_runnable_experiment(project: str, poc: str, dir_tree: dict) -> bool:
+    def is_runnable_experiment(project: str, poc: str, dir_tree: dict[str,dict]) -> bool:
         domains = dir_tree[project][poc]
-        if not (poc_main_path := [paths for domain, paths in domains.items() if 'main' in paths]):
+        # Should have exactly one main folder
+        main_paths = [paths for paths in domains.values() if paths is not None and 'main' in paths.keys()]
+        if len(main_paths) != 1:
             return False
-        if 'index.html' not in poc_main_path[0]['main'].keys():
+        # Main should have index.html
+        if 'index.html' not in main_paths[0]['main'].keys():
             return False
         return True
 
@@ -194,7 +207,7 @@ def get_default_file_content(file_type: str) -> str:
         if file_type != 'py':
             return ''
 
-        with open('experiments/pages/Support/PythonServer/a.test/py-server/index.py', 'r') as file:
+        with open('experiments/pages/Support/PythonServer/a.test/server.py', 'r') as file:
             template_content = file.read()
 
         return template_content
diff --git a/bci/web/blueprints/api.py b/bci/web/blueprints/api.py
index 592fbcab..1828c526 100644
--- a/bci/web/blueprints/api.py
+++ b/bci/web/blueprints/api.py
@@ -16,8 +16,10 @@
 THREAD = None
 
 
-def start_thread(func, args=None) -> bool:
+def __start_thread(func, args=None) -> bool:
     global THREAD
+    if args is None:
+        args = []
     if THREAD and THREAD.is_alive():
         return False
     else:
@@ -26,7 +28,6 @@ def start_thread(func, args=None) -> bool:
         return True
 
 
-
 @api.before_request
 def check_readiness():
     if not bci_api.is_ready():
@@ -55,9 +56,15 @@ def add_headers(response):
 
 @api.route('/evaluation/start/', methods=['POST'])
 def start_evaluation():
+    if request.json is None:
+        return {
+            'status': 'NOK',
+            'msg': "No evaluation parameters found"
+        }
+
     data = request.json.copy()
     params = evaluation_factory(data)
-    if start_thread(bci_api.run, args=[params]):
+    if __start_thread(bci_api.run, args=[params]):
         return {
             'status': 'OK'
         }
@@ -69,6 +76,12 @@ def start_evaluation():
 
 @api.route('/evaluation/stop/', methods=['POST'])
 def stop_evaluation():
+    if request.json is None:
+        return {
+            'status': 'NOK',
+            'msg': "No stop parameters found"
+        }
+
     data = request.json.copy()
     forcefully = data.get('forcefully', False)
     if forcefully:
@@ -140,6 +153,12 @@ def log():
 
 @api.route('/data/', methods=['PUT'])
 def data_source():
+    if request.json is None:
+        return {
+            'status': 'NOK',
+            'msg': "No data parameters found"
+        }
+
     params = request.json.copy()
     revision_data, version_data = bci_api.get_data_sources(params)
     if revision_data or version_data:
@@ -172,30 +191,41 @@ def poc(project: str, poc: str):
     }
 
 
-@api.route('/poc/<string:project>/<string:poc>/<string:domain>/<string:path>/<string:file>/', methods=['GET'])
-def poc_file(project: str, poc: str, domain: str, path: str, file: str):
-    return {
-        'status': 'OK',
-        'content': bci_api.get_poc_file(project, poc, domain, path, file)
-    }
-
-
-@api.route('/poc/<string:project>/<string:poc>/<string:domain>/<string:path>/<string:file>/', methods=['POST'])
-def update_poc_file(project: str, poc: str, domain: str, path: str, file: str):
-    data = request.json.copy()
-    success = bci_api.update_poc_file(project, poc, domain, path, file, data['content'])
-    if success:
+@api.route('/poc/<string:project>/<string:poc>/<string:file>/', methods=['GET', 'POST'])
+def get_poc_file_content(project: str, poc: str, file: str):
+    domain = request.args.get('domain', '')
+    path = request.args.get('path', '')
+    if request.method == 'GET':
         return {
-            'status': 'OK'
-        }
-    else :
-        return {
-            'status': 'NOK'
+            'status': 'OK',
+            'content': bci_api.get_poc_file(project, poc, domain, path, file)
         }
+    else:
+        if not request.json:
+            return {
+                'status': 'NOK',
+                'msg': 'No content to update file with'
+            }
+        data = request.json.copy()
+        success = bci_api.update_poc_file(project, poc, domain, path, file, data['content'])
+        if success:
+            return {
+                'status': 'OK'
+            }
+        else :
+            return {
+                'status': 'NOK'
+            }
 
 
 @api.route('/poc/<string:project>/<string:poc>/', methods=['POST'])
 def add_page(project: str, poc: str):
+    if request.json is None:
+        return {
+            'status': 'NOK',
+            'msg': "No page parameters found"
+        }
+
     data = request.json.copy()
     success = bci_api.add_page(project, poc, data['domain'], data['page'], data['file_type'])
     if success:
@@ -218,6 +248,12 @@ def get_available_domains():
 
 @api.route('/poc/<string:project>/', methods=['POST'])
 def create_experiment(project: str):
+    if request.json is None:
+        return {
+            'status': 'NOK',
+            'msg': "No experiment parameters found"
+        }
+
     data = request.json.copy()
     if 'poc_name' not in data.keys():
         return {
diff --git a/bci/web/blueprints/experiments.py b/bci/web/blueprints/experiments.py
index 2de8daeb..b5cb5945 100644
--- a/bci/web/blueprints/experiments.py
+++ b/bci/web/blueprints/experiments.py
@@ -5,7 +5,7 @@
 import sys
 
 import requests
-from flask import Blueprint, make_response, render_template, request, url_for
+from flask import Blueprint, Request, make_response, render_template, request, url_for
 
 from bci.web.page_parser import load_experiment_pages
 
@@ -26,6 +26,7 @@
 
 @exp.before_request
 def before_request():
+    __report(request)
     host = request.host.lower()
     if host not in ALLOWED_DOMAINS:
         logger.error(
@@ -34,29 +35,13 @@ def before_request():
         return f"Host '{host}' is not supported by this framework."
 
 
-@exp.route("/")
-def index():
-    return f"This page is visited over <b>{request.scheme}</b>."
-
-
-@exp.route("/report/", methods=["GET", "POST"])
-def report():
-    get_params = [item for item in get_all_GET_parameters(request).items()]
-    resp = make_response(
-        render_template("cookies.html", title="Report", get_params=get_params)
-    )
-
-    cookie_exp_date = datetime.datetime.now() + datetime.timedelta(weeks=4)
-    resp.set_cookie("generic", "1", expires=cookie_exp_date)
-    resp.set_cookie("secure", "1", expires=cookie_exp_date, secure=True)
-    resp.set_cookie("httpOnly", "1", expires=cookie_exp_date, httponly=True)
-    resp.set_cookie("lax", "1", expires=cookie_exp_date, samesite="lax")
-    resp.set_cookie("strict", "1", expires=cookie_exp_date, samesite="strict")
-
+def __report(request: Request) -> None:
+    """
+    Submit report to BugHog
+    """
     # Respond to collector on same IP
     # remote_ip = request.remote_addr
     remote_ip = request.headers.get("X-Real-IP")
-
     response_data = {
         "url": request.url,
         "method": request.method,
@@ -72,6 +57,29 @@ def send_report_to_collector():
 
     threading.Thread(target=send_report_to_collector).start()
 
+
+def __get_all_GET_parameters(request) -> dict[str,str]:
+    return {k: v for k, v in request.args.items()}
+
+
+@exp.route("/")
+def index():
+    return f"This page is visited over <b>{request.scheme}</b>."
+
+
+@exp.route("/report/", methods=["GET", "POST"])
+def report_endpoint():
+    get_params = [item for item in __get_all_GET_parameters(request).items()]
+    resp = make_response(
+        render_template("cookies.html", title="Report", get_params=get_params)
+    )
+
+    cookie_exp_date = datetime.datetime.now() + datetime.timedelta(weeks=4)
+    resp.set_cookie("generic", "1", expires=cookie_exp_date)
+    resp.set_cookie("secure", "1", expires=cookie_exp_date, secure=True)
+    resp.set_cookie("httpOnly", "1", expires=cookie_exp_date, httponly=True)
+    resp.set_cookie("lax", "1", expires=cookie_exp_date, samesite="lax")
+    resp.set_cookie("strict", "1", expires=cookie_exp_date, samesite="strict")
     return resp
 
 
@@ -81,7 +89,7 @@ def report_leak_if_using_http(target_scheme):
     Triggers request to /report/ if a request was received over the specified `scheme`.
     """
     used_scheme = request.headers.get("X-Forwarded-Proto")
-    params = get_all_GET_parameters(request)
+    params = __get_all_GET_parameters(request)
     if used_scheme == target_scheme:
         return "Redirect", 307, {"Location": url_for("experiments.report", **params)}
     else:
@@ -96,7 +104,7 @@ def report_leak_if_present(expected_header_name: str):
     if expected_header_name not in request.headers:
         return f"Header {expected_header_name} not found", 200, {"Allow-CSP-From": "*"}
 
-    params = get_all_GET_parameters(request)
+    params = __get_all_GET_parameters(request)
     return (
         "Redirect",
         307,
@@ -121,7 +129,7 @@ def report_leak_if_contains(expected_header_name: str, expected_header_value: st
             {"Allow-CSP-From": "*"},
         )
 
-    params = get_all_GET_parameters(request)
+    params = __get_all_GET_parameters(request)
     return (
         "Redirect",
         307,
@@ -132,15 +140,15 @@ def report_leak_if_contains(expected_header_name: str, expected_header_value: st
     )
 
 
-@exp.route("/<string:project>/<string:experiment>/<string:directory>/")
-def python_evaluation(project: str, experiment: str, directory: str):
+@exp.route("/<string:project>/<string:experiment>/<string:file_name>.py")
+def python_evaluation(project: str, experiment: str, file_name: str):
     """
     Evaluates the python script and returns its result.
     """
     host = request.host.lower()
 
-    module_name = f"{host}/{project}/{experiment}/{directory}"
-    path = f"experiments/pages/{project}/{experiment}/{host}/{directory}/index.py"
+    module_name = f"{host}/{project}/{experiment}"
+    path = f"experiments/pages/{project}/{experiment}/{host}/{file_name}.py"
 
     # Dynamically import the file
     sys.dont_write_bytecode = True
@@ -150,7 +158,3 @@ def python_evaluation(project: str, experiment: str, directory: str):
     spec.loader.exec_module(module)
 
     return module.main(request)
-
-  
-def get_all_GET_parameters(request):
-    return {k: v for k, v in request.args.items()}
diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 59e894fb..278e1189 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -66,8 +66,15 @@
         this.active_file.name = file_name;
         const project = this.project;
         const poc = this.active_poc.name;
-        const path = `/api/poc/${project}/${poc}/${domain}/${file_path}/${file_name}/`;
-        axios.get(path)
+        const params = {};
+        if (domain !== null) {
+          params["domain"] = domain;
+        }
+        if (file_path !== null) {
+          params["path"] = file_path;
+        }
+        const path = `/api/poc/${project}/${poc}/${file_name}/`;
+        axios.get(path, {params: params})
         .then((res) => {
           if (res.data.status === "OK") {
             this.active_file.should_update_server = false;
@@ -101,8 +108,17 @@
           const domain = this.active_poc.active_domain;
           const file_path = this.active_poc.active_path;
           const file_name = this.active_file.name;
-          const path = `/api/poc/${project}/${poc}/${domain}/${file_path}/${file_name}/`;
-          axios.post(path, {"content": this.editor.session.getValue()})
+          const params = {
+            "content": this.editor.session.getValue()
+          };
+          if (domain !== null) {
+            params["domain"] = domain;
+          }
+          if (file_path !== null) {
+            params["path"] = file_path;
+          }
+          const path = `/api/poc/${project}/${poc}/${file_name}/`;
+          axios.post(path, {"content": this.editor.session.getValue()}, {params: params})
           .then((res) => {
             if (res.data.status == "NOK") {
               console.error("Could not update file on server");
@@ -115,7 +131,6 @@
       },
       update_poc_tree(poc_name) {
         const active_poc_name = poc_name === undefined ? this.active_poc.name : poc_name;
-        console.log(active_poc_name);
         const path = `/api/poc/${this.project}/${active_poc_name}/`;
         axios.get(path)
         .then((res) => {
@@ -199,29 +214,60 @@
     <div v-else class="basis-4/12 w-1/12 h-full grow overflow-y-auto">
       <ul class="relative flex flex-col text-gray-700 bg-white shadow-md w-96 rounded-md bg-clip-border dark:bg-dark-3 dark:text-white">
         <nav class="flex min-w-[240px] h-full flex-col gap-1 p-2 font-sans text-base font-normal text-blue-gray-700">
-          <li v-for="([domain, pages, index]) in Object.entries(active_poc.tree)">
-            <ul>
-              <li v-for="([path, files, index]) in Object.entries(pages)">
-                <div class="flex border-b-2 p-2 font-bold mb-2" >
+          <li v-for="([domain, pages]) in Object.entries(active_poc.tree).sort()">
+            <div v-if="domain === 'url_queue.txt'">
+              <div class="flex border-b-2 p-2 font-bold mb-2 hover:bg-gray-100 hover:bg-opacity-80 hover:text-blue-gray-900 hover:cursor-pointer focus:bg-blue-gray-50 focus:bg-opacity-80 focus:text-blue-gray-900" >
+                <div
+                    role="button"
+                    class="rounded-lg"
+                    @click="set_active_file(null, null, domain)"
+                  >
                   <div class="w-full">
-                    {{ domain }}/{{ path }}
+                    {{ domain }}
                   </div>
-                  <a :href="'https://'+domain+'/'+this.project+'/'+this.active_poc.name+'/'+path" target="_blank">
-                    <v-icon name="fa-link" class=""/>
-                  </a>
                 </div>
-                <ul>
-                  <li v-for="file in files"
-                  :class="(domain + '/' + path === this.active_poc.active_domain + '/' + this.active_poc.active_path) && (file === this.active_file.name) ? 'bg-blue-100 dark:bg-blue-900 rounded-lg' : 'rounded-lg'">
-                    <div
+              </div>
+            </div>
+            <ul v-else>
+              <li v-for="([path, files]) in Object.entries(pages).sort()">
+                <div v-if="files">
+                  <div class="flex border-b-2 p-2 font-bold mb-2" >
+                    <div class="w-full">
+                      {{ domain }}/{{ path }}
+                    </div>
+                    <a :href="'https://'+domain+'/'+this.project+'/'+this.active_poc.name+'/'+path" target="_blank">
+                      <v-icon name="fa-link" class=""/>
+                    </a>
+                  </div>
+                  <ul>
+                    <li v-for="([file, _]) in Object.entries(files)"
+                    :class="(domain + '/' + path === this.active_poc.active_domain + '/' + this.active_poc.active_path) && (file === this.active_file.name) ? 'bg-blue-100 dark:bg-blue-900 rounded-lg' : 'rounded-lg'">
+                      <div
+                        role="button"
+                        class="flex items-center indent-4 w-full p-2 hover:bg-gray-100 hover:bg-opacity-80 hover:text-blue-gray-900 hover:cursor-pointer focus:bg-blue-gray-50 focus:bg-opacity-80 focus:text-blue-gray-900 rounded-lg"
+                        @click="set_active_file(domain, path, file)"
+                      >
+                        {{ file }}
+                      </div>
+                    </li>
+                  </ul>
+                </div>
+                <div class="flex justify-between border-b-2 p-2 font-bold mb-2 hover:bg-gray-100 hover:bg-opacity-80 hover:text-blue-gray-900 hover:cursor-pointer focus:bg-blue-gray-50 focus:bg-opacity-80 focus:text-blue-gray-900" v-else>
+                  <div
                       role="button"
-                      class="flex items-center indent-4 w-full p-2 hover:bg-gray-100 hover:bg-opacity-80 hover:text-blue-gray-900 hover:cursor-pointer focus:bg-blue-gray-50 focus:bg-opacity-80 focus:text-blue-gray-900 rounded-lg"
-                      @click="set_active_file(domain, path, file)"
+                      class="rounded-lg"
+                      @click="set_active_file(domain, null, path)"
                     >
-                      {{ file }}
+                    <div class="w-full">
+                      {{ domain }}/{{ path }}
                     </div>
-                  </li>
-                </ul>
+                  </div>
+                  <div>
+                    <a :href="'https://'+domain+'/'+this.project+'/'+this.active_poc.name+'/'+path" target="_blank">
+                      <v-icon name="fa-link" class=""/>
+                    </a>
+                  </div>
+                </div>
               </li>
             </ul>
           </li>
diff --git a/experiments/pages/Support/PythonServer/a.test/py-server/index.py b/experiments/pages/Support/PythonServer/a.test/server.py
similarity index 98%
rename from experiments/pages/Support/PythonServer/a.test/py-server/index.py
rename to experiments/pages/Support/PythonServer/a.test/server.py
index 91e823b8..fb47ecdb 100644
--- a/experiments/pages/Support/PythonServer/a.test/py-server/index.py
+++ b/experiments/pages/Support/PythonServer/a.test/server.py
@@ -12,4 +12,4 @@ def main(req: Request):
         "path": req.path,
         "scheme": req.scheme,
         "url": req.url
-    }
\ No newline at end of file
+    }
diff --git a/nginx/config/experiments.conf b/nginx/config/experiments.conf
index 398dac9c..9ac74009 100644
--- a/nginx/config/experiments.conf
+++ b/nginx/config/experiments.conf
@@ -1,6 +1,15 @@
 access_log /logs/nginx-access-poc.log default_format;
 
-location /res/ {
+# Home
+location = / {
+    proxy_pass http://core:5000;
+    proxy_set_header Host $host;
+    proxy_set_header X-Real-IP $remote_addr;
+    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+}
+
+# Shared static resources
+location ^~ /res/ {
     include /etc/nginx/config/notify_collector.conf;
     error_page 504 @resources;
 }
@@ -9,11 +18,8 @@ location @resources {
     root /www/data;
 }
 
-location ~ index\.(.+)$ {
-    root /www/data/pages;
-}
-
-location ~ ^/report(/.+)*/?$ {
+# Reporting endpoint
+location ~ /report/?[^/]*$ {
     proxy_pass http://core:5000;
     proxy_set_header Host $host;
     proxy_set_header X-Real-IP $remote_addr;
@@ -21,7 +27,8 @@ location ~ ^/report(/.+)*/?$ {
     proxy_set_header X-Forwarded-Proto $scheme;
 }
 
-location ~ ^/(.+)/(.+)/py-(.+)/$ {
+# Dynamic experiment resources
+location ~ (.+).py$ {
     proxy_pass http://core:5000;
     proxy_set_header Host $host;
     proxy_set_header X-Real-IP $remote_addr;
@@ -29,11 +36,21 @@ location ~ ^/(.+)/(.+)/py-(.+)/$ {
     proxy_set_header X-Forwarded-Proto $scheme;
 }
 
-location ~ ^/(.+)/(.+)/(.+)/$ {
+# Static experiment resources
+location ~ index\.(html|js)$ {
+    root /www/data/pages;
+}
+
+location ~ ^/[^/]+/[^/]+/[^/]+/?$ {
+    include /etc/nginx/config/notify_collector.conf;
+    error_page 504 @experiment;
+}
+
+location @experiment {
     root /www/data/pages;
     index index.html index.js;
     # Rewrite URLs conform to experiment file structure
-    rewrite ^/(.+)/(.+)/(.+)/$ /$1/$2/$host/$3/ break;
+    rewrite ^/([^/]+)/([^/]+)/([^/]+)/?$ /$1/$2/$host/$3/ break;
     # Add experiment headers
     access_by_lua_block {
         local cjson = require "cjson"
@@ -59,19 +76,3 @@ location ~ ^/(.+)/(.+)/(.+)/$ {
         end
     }
 }
-
-location ~ ^/(.+)/(.+)/(.+)$ {
-    include /etc/nginx/config/notify_collector.conf;
-    error_page 504 @experiment;
-}
-
-location @experiment {
-    rewrite ^/(.+)$ /$1/;
-}
-
-location / {
-    proxy_pass http://core:5000;
-    proxy_set_header Host $host;
-    proxy_set_header X-Real-IP $remote_addr;
-    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
-}

From 44e5dac47981a39b41e81bf5354538c7255781ac Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 12:15:44 +0000
Subject: [PATCH 18/57] Editing config files through the web UI

---
 bci/evaluations/custom/custom_evaluation.py | 17 ++++---
 bci/web/vue/src/components/poc-editor.vue   | 51 ++++++++++++++++++---
 2 files changed, 54 insertions(+), 14 deletions(-)

diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index b2d97ef3..8e81ed90 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -25,11 +25,7 @@ def initialize_dir_tree() -> dict:
 
         def path_to_dict(path):
             if os.path.isdir(path):
-                return {
-                    sub_folder: path_to_dict(os.path.join(path, sub_folder))
-                    for sub_folder in os.listdir(path)
-                    if sub_folder != 'url_queue.txt'
-                }
+                return {sub_folder: path_to_dict(os.path.join(path, sub_folder)) for sub_folder in os.listdir(path)}
             else:
                 return os.path.basename(path)
 
@@ -154,15 +150,22 @@ def get_projects(self) -> list[str]:
     def get_poc_structure(self, project: str, poc: str) -> dict:
         return self.dir_tree[project][poc]
 
+    def _get_poc_file_path(self, project: str, poc: str, domain: str, path: str, file_name: str) -> str:
+        # Top-level config file
+        if domain == 'Config' and path == '_':
+            return os.path.join(Global.custom_page_folder, project, poc, file_name)
+
+        return os.path.join(Global.custom_page_folder, project, poc, domain, path, file_name)
+
     def get_poc_file(self, project: str, poc: str, domain: str, path: str, file_name: str) -> str:
-        file_path = os.path.join(Global.custom_page_folder, project, poc, domain, path, file_name)
+        file_path = self._get_poc_file_path(project, poc, domain, path, file_name)
         if os.path.isfile(file_path):
             with open(file_path) as file:
                 return file.read()
         raise AttributeError(f"Could not find PoC file at expected path '{file_path}'")
 
     def update_poc_file(self, project: str, poc: str, domain: str, path: str, file_name: str, content: str) -> bool:
-        file_path = os.path.join(Global.custom_page_folder, project, poc, domain, path, file_name)
+        file_path = self._get_poc_file_path(project, poc, domain, path, file_name)
         if os.path.isfile(file_path):
             if content == '':
                 logger.warning('Attempt to save empty file ignored')
diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 59e894fb..53a2eaac 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -37,6 +37,7 @@
             //     "path1": ["file1", "file2"],
             //     "path2": ["file1"],
             //   },
+            //  'interaction_script.cmd': 'interaction_script.cmd',
             // },
         },
         available_file_types: [
@@ -44,6 +45,10 @@
           'js',
           'py',
         ],
+        poc_tree_config: {
+          domain: 'Config',
+          page: '_',
+        },
         dialog: {
           domain: {
             name: null,
@@ -59,6 +64,33 @@
         timeout: null,
       }
     },
+    computed: {
+      active_poc_tree() {
+        return Object.entries(this.active_poc.tree).reduce((acc, [domain, pages]) => {
+          if (domain !== pages) {
+            return [
+              ...acc,
+              [domain, pages]
+            ]
+          }
+
+          const configDomain = this.poc_tree_config.domain;
+          const configPage = this.poc_tree_config.page;
+
+          // A single top-level file -> create a virtual config folder
+          const config_folder = acc.find(([domain]) => domain === configDomain) ?? [configDomain, {[configPage]: {}}];
+          return [
+            ...acc.filter(([domain]) => domain !== configDomain),
+            [configDomain, {
+              [configPage]: {
+                ...config_folder[1].subfolder,
+                [domain]: pages,
+              }
+            }],
+          ]
+        }, []);
+      }
+    },
     methods: {
       set_active_file(domain, file_path, file_name) {
         this.active_poc.active_domain = domain;
@@ -199,16 +231,21 @@
     <div v-else class="basis-4/12 w-1/12 h-full grow overflow-y-auto">
       <ul class="relative flex flex-col text-gray-700 bg-white shadow-md w-96 rounded-md bg-clip-border dark:bg-dark-3 dark:text-white">
         <nav class="flex min-w-[240px] h-full flex-col gap-1 p-2 font-sans text-base font-normal text-blue-gray-700">
-          <li v-for="([domain, pages, index]) in Object.entries(active_poc.tree)">
+          <li v-for="([domain, pages, index]) in active_poc_tree">
             <ul>
               <li v-for="([path, files, index]) in Object.entries(pages)">
                 <div class="flex border-b-2 p-2 font-bold mb-2" >
-                  <div class="w-full">
-                    {{ domain }}/{{ path }}
-                  </div>
-                  <a :href="'https://'+domain+'/'+this.project+'/'+this.active_poc.name+'/'+path" target="_blank">
-                    <v-icon name="fa-link" class=""/>
-                  </a>
+                  <template v-if="domain !== poc_tree_config.domain">
+                    <div class="w-full">
+                      {{ domain }}/{{ path }}
+                    </div>
+                    <a :href="'https://'+domain+'/'+this.project+'/'+this.active_poc.name+'/'+path" target="_blank">
+                      <v-icon name="fa-link" class=""/>
+                    </a>
+                  </template>
+                  <template v-else>
+                    {{ domain}}
+                  </template>
                 </div>
                 <ul>
                   <li v-for="file in files"

From 025c8ec4824f1ea9df6cded65978c7bc074c3739 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 12:27:47 +0000
Subject: [PATCH 19/57] Interaction script - support blank lines and comments

---
 bci/browser/interaction/interaction.py                   | 9 ++++++---
 experiments/pages/Support/AutoGUI/interaction_script.cmd | 2 ++
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index e84c4328..6177983c 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -1,11 +1,8 @@
 import logging
-import re
 from inspect import signature
 
 from bci.browser.configuration.browser import Browser as BrowserConfig
 from bci.browser.interaction.browsers.browser import Browser
-from bci.browser.interaction.browsers.chromium import Chromium
-from bci.browser.interaction.browsers.firefox import Firefox
 
 logger = logging.getLogger(__name__)
 
@@ -50,9 +47,15 @@ def _initiate_browser(self) -> Browser:
 
     def _interpret(self, browser: Browser) -> None:
         for statement in self.script:
+            if statement.strip() == '':
+                continue
+
             cmd, *args = statement.split()
             method_name = cmd.lower()
 
+            if cmd == '#':
+                continue
+
             if method_name not in Browser.public_methods:
                 raise Exception(
                     f'Invalid command `{cmd}`. Expected one of {", ".join(map(lambda m: m.upper(), Browser.public_methods))}.'
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/interaction_script.cmd
index 92690174..26ec60ca 100644
--- a/experiments/pages/Support/AutoGUI/interaction_script.cmd
+++ b/experiments/pages/Support/AutoGUI/interaction_script.cmd
@@ -1,2 +1,4 @@
 NAVIGATE https://a.test/Support/AutoGUI/main
+
+# test
 CLICK 100 100
\ No newline at end of file

From 32a61492a9360933859b62ddf54b02487caa47f9 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 13:19:20 +0000
Subject: [PATCH 20/57] Interaction script editor code highlighting

---
 bci/web/vue/src/components/poc-editor.vue  |  4 ++
 bci/web/vue/src/interaction_script_mode.js | 47 ++++++++++++++++++++++
 2 files changed, 51 insertions(+)
 create mode 100644 bci/web/vue/src/interaction_script_mode.js

diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 53a2eaac..48253620 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -4,6 +4,7 @@
   import { Mode as JsMode } from 'ace-builds/src-noconflict/mode-javascript';
   import { Mode as JsonMode } from 'ace-builds/src-noconflict/mode-json';
   import { Mode as PyMode } from 'ace-builds/src-noconflict/mode-python';
+  import { getMode as getInteractionScriptMode } from '../interaction_script_mode';
   import 'ace-builds/src-min-noconflict/ext-modelist';
   import 'ace-builds/src-min-noconflict/theme-twilight';
   import 'ace-builds/src-min-noconflict/theme-xcode';
@@ -175,6 +176,9 @@
           case "py":
             this.editor.session.setMode(new PyMode());
             break;
+          case "cmd":
+            getInteractionScriptMode().then(({ Mode }) => { this.editor.session.setMode(new Mode()) })
+            break;
         }
       },
       add_page() {
diff --git a/bci/web/vue/src/interaction_script_mode.js b/bci/web/vue/src/interaction_script_mode.js
new file mode 100644
index 00000000..fb697e44
--- /dev/null
+++ b/bci/web/vue/src/interaction_script_mode.js
@@ -0,0 +1,47 @@
+const KEYWORDS = "NAVIGATE|CLICK";
+
+ace.define("ace/mode/interaction_script_highlight_rules",["require","exports","module","ace/lib/oop","ace/mode/text_highlight_rules"], function(require, exports, module){"use strict";
+    const oop = require("../lib/oop");
+    const TextHighlightRules = require("./text_highlight_rules").TextHighlightRules;
+
+    const HighlightRules = function() {
+
+        var keywordMapper = this.createKeywordMapper({
+            "keyword": KEYWORDS,
+        }, "argument", true);
+
+        this.$rules = {
+            "start" : [ {
+                token : "comment",
+                regex : "#.*$"
+            }, {
+                token : "constant.numeric", // float
+                regex : "[+-]?\\d+(?:(?:\\.\\d*)?(?:[eE][+-]?\\d+)?)?\\b"
+            }, {
+                token : keywordMapper,
+                regex : "[a-zA-Z_$][a-zA-Z0-9_$]*\\b"
+            } ]
+        };
+        this.normalizeRules();
+    };
+
+    oop.inherits(HighlightRules, TextHighlightRules);
+    exports.HighlightRules = HighlightRules;
+});
+
+ace.define("ace/mode/interaction_script",["require","exports","module","ace/lib/oop","ace/mode/text", "ace/mode/interaction_script_highlight_rules"], function(require, exports){"use strict";
+    const oop = require("ace/lib/oop");
+    const TextMode = require("ace/mode/text").Mode;
+    const HighlightRules = require("ace/mode/interaction_script_highlight_rules").HighlightRules;
+    const Mode = function() {
+        this.HighlightRules = HighlightRules;
+    };
+    oop.inherits(Mode, TextMode);
+    exports.Mode = Mode;
+});
+
+const getMode = () => new Promise((resolve) => ace.require(["ace/mode/interaction_script"], resolve));
+
+export {
+    getMode,
+};
\ No newline at end of file

From b56b17c29602b2d6167b795ef8c734735aa784f1 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 13:58:22 +0000
Subject: [PATCH 21/57] Add new Sleep command

---
 bci/browser/interaction/browsers/__init__.py  |  0
 bci/browser/interaction/browsers/chromium.py  | 51 -------------
 bci/browser/interaction/browsers/firefox.py   | 75 -------------------
 bci/browser/interaction/interaction.py        | 40 +++-------
 .../{browsers/browser.py => simulation.py}    | 19 ++---
 bci/web/vue/src/interaction_script_mode.js    |  2 +-
 .../Support/AutoGUI/interaction_script.cmd    |  4 +-
 7 files changed, 23 insertions(+), 168 deletions(-)
 delete mode 100644 bci/browser/interaction/browsers/__init__.py
 delete mode 100644 bci/browser/interaction/browsers/chromium.py
 delete mode 100644 bci/browser/interaction/browsers/firefox.py
 rename bci/browser/interaction/{browsers/browser.py => simulation.py} (79%)

diff --git a/bci/browser/interaction/browsers/__init__.py b/bci/browser/interaction/browsers/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/bci/browser/interaction/browsers/chromium.py b/bci/browser/interaction/browsers/chromium.py
deleted file mode 100644
index 7db878af..00000000
--- a/bci/browser/interaction/browsers/chromium.py
+++ /dev/null
@@ -1,51 +0,0 @@
-from time import sleep
-
-from .browser import Browser
-
-
-class Chromium(Browser):
-    session_id: str
-
-    def get_ws_endpoint(self, host: str, port: int, browser_id: str) -> str:
-        return f'ws://{host}:{port}/devtools/browser/{browser_id}'
-
-    def initialize_connection(self, browserId, port, host):
-        # Get list of all targets and find a "page" target.
-        target_response = self.send(
-            {
-                'method': 'Target.getTargets',
-            }
-        )
-
-        page_target = list(filter(lambda info: (info['type'] == 'page'), target_response['result']['targetInfos']))[0][
-            'targetId'
-        ]
-
-        # Attach to the page target.
-        session = self.send({'method': 'Target.attachToTarget', 'params': {'targetId': page_target, 'flatten': True}})
-
-        self.session_id = session['result']['sessionId']
-
-    def close_connection(self):
-        pass
-
-    def navigate(self, url):
-        self.send({'sessionId': self.session_id, 'method': 'Page.navigate', 'params': {'url': url}})
-        sleep(0.5)
-
-    def click(self, x, y):
-        self.send(
-            {
-                'sessionId': self.session_id,
-                'method': 'Input.dispatchMouseEvent',
-                'params': {'x': x, 'y': y, 'type': 'mousePressed', 'clickCount': 1, 'button': 'left'},
-            }
-        )
-
-        self.send(
-            {
-                'sessionId': self.session_id,
-                'method': 'Input.dispatchMouseEvent',
-                'params': {'x': x, 'y': y, 'type': 'mouseReleased', 'button': 'left'},
-            }
-        )
diff --git a/bci/browser/interaction/browsers/firefox.py b/bci/browser/interaction/browsers/firefox.py
deleted file mode 100644
index 9f5d6f02..00000000
--- a/bci/browser/interaction/browsers/firefox.py
+++ /dev/null
@@ -1,75 +0,0 @@
-from .browser import Browser
-
-
-class Firefox(Browser):
-    browsing_context: str
-
-    def get_ws_endpoint(self, host: str, port: int, browser_id: str) -> str:
-        return f'ws://{host}:{port}/session'
-
-    def initialize_connection(self, browserId, port, host):
-        # Initiate the session
-        session_id = self.send({'method': 'session.new', 'params': {'capabilities': {}}})['result']['sessionId']
-
-        # Subscribe to browser events
-        self.send(
-            {
-                'method': 'session.subscribe',
-                'params': {
-                    'events': [
-                        'browsingContext.domContentLoaded',
-                    ]
-                },
-            }
-        )
-
-        # Create the browsing context
-        user_context = self.send({'method': 'browser.createUserContext', 'params': {}})['result']['userContext']
-
-        self.browsing_context = self.send(
-            {'method': 'browsingContext.create', 'params': {'type': 'tab', 'userContext': user_context}}
-        )['result']['context']
-
-    def close_connection(self):
-        self.send(
-            {
-                'method': 'session.end',
-                'params': {},
-            }
-        )
-
-    def navigate(self, url):
-        navigation = self.send(
-            {'method': 'browsingContext.navigate', 'params': {'url': url, 'context': self.browsing_context}}
-        )['result']['navigation']
-
-        # Wait for the DOM to load
-        self.listen(
-            'browsingContext.domContentLoaded',
-            {}
-            #{
-            #    'url': url,
-            #    'context': self.browsing_context,
-            #    'navigation': navigation,
-            #},
-        )
-
-    def click(self, x, y):
-        self.send(
-            {
-                'method': 'input.performActions',
-                'params': {
-                    'context': self.browsing_context,
-                    'actions': [
-                        {
-                            'type': 'pointer',
-                            'id': str(self.req_id()),
-                            'actions': [
-                                {'type': 'pointerDown', 'button': 1, 'width': x, 'height': y},
-                                {'type': 'pointerUp', 'button': 1, 'width': x, 'height': y},
-                            ],
-                        }
-                    ],
-                },
-            }
-        )
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index 6177983c..4f4e9dd3 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -2,7 +2,7 @@
 from inspect import signature
 
 from bci.browser.configuration.browser import Browser as BrowserConfig
-from bci.browser.interaction.browsers.browser import Browser
+from bci.browser.interaction.simulation import Simulation
 
 logger = logging.getLogger(__name__)
 
@@ -16,36 +16,18 @@ def __init__(self, browser: BrowserConfig, script: list[str]) -> None:
         self.script = script
 
     def execute(self) -> None:
-        interaction_browser = self._initiate_browser()
+        simulation = self._initiate_simulation()
 
-        self._interpret(interaction_browser)
+        self._interpret(simulation)
 
-        interaction_browser.navigate('https://a.test/report/?bughog_sanity_check=OK')
+        simulation.navigate('https://a.test/report/?bughog_sanity_check=OK')
+        simulation.sleep('0.5')
 
-    def _initiate_browser(self) -> Browser:
+    def _initiate_simulation(self) -> Simulation:
         # TODO - possibly return different browser instances
-        return Browser(self.browser)
-        """
-        cdp = re.search(
-            r'DevTools listening on ws:\/\/(.+):(.+)\/devtools\/browser\/(.+)\n',
-            init_output,
-        )
+        return Simulation(self.browser)
 
-        if cdp:
-            return Chromium(browser_id=cdp.group(3), port=int(cdp.group(2)), host=cdp.group(1))
-
-        bidi = re.search(
-            r'WebDriver BiDi listening on ws:\/\/(.+):(.+)',
-            init_output,
-        )
-
-        if bidi:
-            return Firefox(port=int(bidi.group(2)), host=bidi.group(1))
-
-        raise Exception('Unrecognized browser')
-        """
-
-    def _interpret(self, browser: Browser) -> None:
+    def _interpret(self, simulation: Simulation) -> None:
         for statement in self.script:
             if statement.strip() == '':
                 continue
@@ -56,12 +38,12 @@ def _interpret(self, browser: Browser) -> None:
             if cmd == '#':
                 continue
 
-            if method_name not in Browser.public_methods:
+            if method_name not in Simulation.public_methods:
                 raise Exception(
-                    f'Invalid command `{cmd}`. Expected one of {", ".join(map(lambda m: m.upper(), Browser.public_methods))}.'
+                    f'Invalid command `{cmd}`. Expected one of {", ".join(map(lambda m: m.upper(), Simulation.public_methods))}.'
                 )
 
-            method = getattr(browser, method_name)
+            method = getattr(simulation, method_name)
             method_params_len = len(signature(method).parameters)
 
             if method_params_len != len(args):
diff --git a/bci/browser/interaction/browsers/browser.py b/bci/browser/interaction/simulation.py
similarity index 79%
rename from bci/browser/interaction/browsers/browser.py
rename to bci/browser/interaction/simulation.py
index 2d45dafd..80ff17e5 100644
--- a/bci/browser/interaction/browsers/browser.py
+++ b/bci/browser/interaction/simulation.py
@@ -10,9 +10,9 @@
 from bci.browser.configuration.browser import Browser as BrowserConfig
 
 
-class Browser:
+class Simulation:
     browser_config: BrowserConfig
-    public_methods: list[str] = ['navigate', 'click']
+    public_methods: list[str] = ['navigate', 'click', 'sleep']
 
     def __init__(self, browser_config: BrowserConfig):
         self.browser_config = browser_config
@@ -28,20 +28,17 @@ def navigate(self, url: str):
         self.browser_config.terminate()
         self.browser_config.open(url)
 
-        # TODO - convert this into an argument or a separate command
-        sleep(2)
-
     def click(self, x: str, y: str):
-        # print(gui.size())
-        # print(gui.position())
-        # gui.moveTo(int(x), int(y))
-
         gui.moveTo(100, 540)
         gui.click()
 
+    def sleep(self, duration: str):
+        sleep(float(duration))
+
+    def screenshot(self):
+        # TODO
         # buffered = BytesIO()
         # print(gui.screenshot().save(buffered, format='JPEG'))
         # img_str = base64.b64encode(buffered.getvalue())
         # print(img_str.decode('utf-8'))
-
-        sleep(0.5)
+        pass
diff --git a/bci/web/vue/src/interaction_script_mode.js b/bci/web/vue/src/interaction_script_mode.js
index fb697e44..27fd0d9b 100644
--- a/bci/web/vue/src/interaction_script_mode.js
+++ b/bci/web/vue/src/interaction_script_mode.js
@@ -1,4 +1,4 @@
-const KEYWORDS = "NAVIGATE|CLICK";
+const KEYWORDS = "NAVIGATE|CLICK|SLEEP";
 
 ace.define("ace/mode/interaction_script_highlight_rules",["require","exports","module","ace/lib/oop","ace/mode/text_highlight_rules"], function(require, exports, module){"use strict";
     const oop = require("../lib/oop");
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/interaction_script.cmd
index 26ec60ca..43d2d731 100644
--- a/experiments/pages/Support/AutoGUI/interaction_script.cmd
+++ b/experiments/pages/Support/AutoGUI/interaction_script.cmd
@@ -1,4 +1,6 @@
 NAVIGATE https://a.test/Support/AutoGUI/main
+SLEEP 0.5
 
 # test
-CLICK 100 100
\ No newline at end of file
+CLICK 100 540
+SLEEP 1
\ No newline at end of file

From 47757967ebe650b2618624e226b2402fc03b07be Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 14:41:45 +0000
Subject: [PATCH 22/57] Clicking on element IDs

---
 bci/browser/interaction/elements/five.png     | Bin 0 -> 4220 bytes
 bci/browser/interaction/elements/four.png     | Bin 0 -> 4220 bytes
 bci/browser/interaction/elements/one.png      | Bin 0 -> 4219 bytes
 bci/browser/interaction/elements/six.png      | Bin 0 -> 4219 bytes
 bci/browser/interaction/elements/three.png    | Bin 0 -> 4220 bytes
 bci/browser/interaction/elements/two.png      | Bin 0 -> 4220 bytes
 bci/browser/interaction/simulation.py         |  20 +++---
 bci/web/vue/src/interaction_script_mode.js    |   2 +-
 .../Support/AutoGUI/a.test/main/index.html    |  63 +++++++++++++++++-
 .../Support/AutoGUI/interaction_script.cmd    |   8 ++-
 experiments/res/bughog.css                    |  58 ++++++++++++++++
 11 files changed, 138 insertions(+), 13 deletions(-)
 create mode 100644 bci/browser/interaction/elements/five.png
 create mode 100644 bci/browser/interaction/elements/four.png
 create mode 100644 bci/browser/interaction/elements/one.png
 create mode 100644 bci/browser/interaction/elements/six.png
 create mode 100644 bci/browser/interaction/elements/three.png
 create mode 100644 bci/browser/interaction/elements/two.png
 create mode 100644 experiments/res/bughog.css

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diff --git a/bci/browser/interaction/elements/two.png b/bci/browser/interaction/elements/two.png
new file mode 100644
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diff --git a/bci/browser/interaction/simulation.py b/bci/browser/interaction/simulation.py
index 80ff17e5..c87fa39b 100644
--- a/bci/browser/interaction/simulation.py
+++ b/bci/browser/interaction/simulation.py
@@ -12,7 +12,7 @@
 
 class Simulation:
     browser_config: BrowserConfig
-    public_methods: list[str] = ['navigate', 'click', 'sleep']
+    public_methods: list[str] = ['navigate', 'click', 'click_el', 'sleep', 'screenshot']
 
     def __init__(self, browser_config: BrowserConfig):
         self.browser_config = browser_config
@@ -29,16 +29,20 @@ def navigate(self, url: str):
         self.browser_config.open(url)
 
     def click(self, x: str, y: str):
-        gui.moveTo(100, 540)
+        gui.moveTo(int(x), int(y))
         gui.click()
 
+    def click_el(self, el_id: str):
+        el_image_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), f'elements/{el_id}.png')
+        x, y = gui.locateCenterOnScreen(el_image_path)
+        self.click(str(x), str(y))
+
     def sleep(self, duration: str):
         sleep(float(duration))
 
     def screenshot(self):
-        # TODO
-        # buffered = BytesIO()
-        # print(gui.screenshot().save(buffered, format='JPEG'))
-        # img_str = base64.b64encode(buffered.getvalue())
-        # print(img_str.decode('utf-8'))
-        pass
+        # TODO save to the filesystem
+        buffered = BytesIO()
+        print(gui.screenshot().save(buffered, format='JPEG'))
+        img_str = base64.b64encode(buffered.getvalue())
+        print(img_str.decode('utf-8'))
diff --git a/bci/web/vue/src/interaction_script_mode.js b/bci/web/vue/src/interaction_script_mode.js
index 27fd0d9b..35785b44 100644
--- a/bci/web/vue/src/interaction_script_mode.js
+++ b/bci/web/vue/src/interaction_script_mode.js
@@ -1,4 +1,4 @@
-const KEYWORDS = "NAVIGATE|CLICK|SLEEP";
+const KEYWORDS = "NAVIGATE|CLICK|CLICK_EL|SLEEP|SCREENSHOT";
 
 ace.define("ace/mode/interaction_script_highlight_rules",["require","exports","module","ace/lib/oop","ace/mode/text_highlight_rules"], function(require, exports, module){"use strict";
     const oop = require("../lib/oop");
diff --git a/experiments/pages/Support/AutoGUI/a.test/main/index.html b/experiments/pages/Support/AutoGUI/a.test/main/index.html
index 4c9318e8..fabffa1b 100644
--- a/experiments/pages/Support/AutoGUI/a.test/main/index.html
+++ b/experiments/pages/Support/AutoGUI/a.test/main/index.html
@@ -1 +1,62 @@
-<a href="https://a.test/report/?leak=AutoGUI" style="position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: red;">CLICK</a>
\ No newline at end of file
+<link rel="stylesheet" href="https://a.test/res/bughog.css">
+<style>
+.fullscreen {
+    position: fixed;
+    top: 0;
+    left: 0;
+    width: 100%;
+    height: 100%;
+    background-color: red;
+    z-index: 10;
+}
+
+#one, #two, #three, #four, #five, #six {
+    position: fixed;
+    width: 25px;
+    height: 20px;
+    font-size: 0;
+}
+
+#one {
+    background-color: #800000;
+    color: #800000;
+    top: 10px;
+    left: 10px;
+}
+
+#two {
+    background-color: #dcbeff;
+    color: #dcbeff;
+    top: 45px;
+    left: 10px;
+}
+
+#three {
+    background-color: #ffe119;
+    color: #ffe119;
+    top: 80px;
+    left: 10px;
+}
+
+#four {
+    background-color: #4363d8;
+    color: #4363d8;
+    top: 10px;
+    left: 45px;
+}
+
+#five {
+    background-color: #f58231;
+    color: #f58231;
+    top: 45px;
+    left: 45px;
+}
+
+#six {
+    background-color: #000075;
+    color: #000075;
+    top: 80px;
+    left: 45px;
+}
+</style>
+<a href="https://a.test/report/?leak=AutoGUI" id="three">CLICK</a>
\ No newline at end of file
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/interaction_script.cmd
index 43d2d731..8aaa6b70 100644
--- a/experiments/pages/Support/AutoGUI/interaction_script.cmd
+++ b/experiments/pages/Support/AutoGUI/interaction_script.cmd
@@ -1,6 +1,8 @@
 NAVIGATE https://a.test/Support/AutoGUI/main
-SLEEP 0.5
+SLEEP 1
 
-# test
-CLICK 100 540
+SCREENSHOT
+
+# Comment
+CLICK_EL three
 SLEEP 1
\ No newline at end of file
diff --git a/experiments/res/bughog.css b/experiments/res/bughog.css
new file mode 100644
index 00000000..10be4b2d
--- /dev/null
+++ b/experiments/res/bughog.css
@@ -0,0 +1,58 @@
+.fullscreen {
+    position: fixed;
+    top: 0;
+    left: 0;
+    width: 100%;
+    height: 100%;
+    background-color: red;
+    z-index: 10;
+}
+
+#one, #two, #three, #four, #five, #six {
+    position: fixed;
+    width: 25px;
+    height: 20px;
+    font-size: 0;
+}
+
+#one {
+    background-color: #800000;
+    color: #800000;
+    top: 10px;
+    left: 10px;
+}
+
+#two {
+    background-color: #dcbeff;
+    color: #dcbeff;
+    top: 45px;
+    left: 10px;
+}
+
+#three {
+    background-color: #ffe119;
+    color: #ffe119;
+    top: 80px;
+    left: 10px;
+}
+
+#four {
+    background-color: #4363d8;
+    color: #4363d8;
+    top: 10px;
+    left: 45px;
+}
+
+#five {
+    background-color: #f58231;
+    color: #f58231;
+    top: 45px;
+    left: 45px;
+}
+
+#six {
+    background-color: #000075;
+    color: #000075;
+    top: 80px;
+    left: 45px;
+}
\ No newline at end of file

From 641f122724e6e05ffc28fa3e8cc83402ecfa879c Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 14:48:21 +0000
Subject: [PATCH 23/57] Implement clicking by screen percentage

---
 bci/browser/interaction/simulation.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/bci/browser/interaction/simulation.py b/bci/browser/interaction/simulation.py
index c87fa39b..8548d2cf 100644
--- a/bci/browser/interaction/simulation.py
+++ b/bci/browser/interaction/simulation.py
@@ -23,13 +23,23 @@ def __init__(self, browser_config: BrowserConfig):
     def __del__(self):
         self.browser_config.terminate()
 
+    def parse_position(self, position: str, max_value: int) -> int:
+        # Screen percentage
+        if position[-1] == '%':
+            return round(max_value * (int(position[:-1]) / 100))
+
+        # Absolute value in pixels
+        return int(position)
+
     # --- PUBLIC METHODS ---
     def navigate(self, url: str):
         self.browser_config.terminate()
         self.browser_config.open(url)
 
     def click(self, x: str, y: str):
-        gui.moveTo(int(x), int(y))
+        max_x, max_y = gui.size()
+
+        gui.moveTo(self.parse_position(x, max_x), self.parse_position(y, max_y))
         gui.click()
 
     def click_el(self, el_id: str):

From 3ede69e7248ba241990ad94d730d4c002fe70959 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 14:48:32 +0000
Subject: [PATCH 24/57] Implement clicking by screen percentage

---
 experiments/pages/Support/AutoGUI/a.test/main/index.html | 2 +-
 experiments/pages/Support/AutoGUI/interaction_script.cmd | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/experiments/pages/Support/AutoGUI/a.test/main/index.html b/experiments/pages/Support/AutoGUI/a.test/main/index.html
index fabffa1b..f7700d53 100644
--- a/experiments/pages/Support/AutoGUI/a.test/main/index.html
+++ b/experiments/pages/Support/AutoGUI/a.test/main/index.html
@@ -59,4 +59,4 @@
     left: 45px;
 }
 </style>
-<a href="https://a.test/report/?leak=AutoGUI" id="three">CLICK</a>
\ No newline at end of file
+<a href="https://a.test/report/?leak=AutoGUI" class="fullscreen">CLICK</a>
\ No newline at end of file
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/interaction_script.cmd
index 8aaa6b70..f98842c0 100644
--- a/experiments/pages/Support/AutoGUI/interaction_script.cmd
+++ b/experiments/pages/Support/AutoGUI/interaction_script.cmd
@@ -3,6 +3,6 @@ SLEEP 1
 
 SCREENSHOT
 
-# Comment
-CLICK_EL three
+# test
+CLICK 200 50%
 SLEEP 1
\ No newline at end of file

From 8e1043a2dc7181de7b842f8c7450953e9a9a1a43 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Thu, 31 Oct 2024 15:08:51 +0000
Subject: [PATCH 25/57] Save screenshots to filesystem

---
 .gitignore                                     | 11 +++++++++++
 bci/browser/interaction/interaction.py         | 11 +++++------
 bci/browser/interaction/simulation.py          | 18 +++++++++---------
 bci/evaluations/custom/custom_evaluation.py    |  2 +-
 .../Support/AutoGUI/a.test/main/index.html     |  2 +-
 .../Support/AutoGUI/interaction_script.cmd     |  7 ++-----
 logs/screenshots/.gitkeep                      |  0
 7 files changed, 29 insertions(+), 22 deletions(-)
 create mode 100644 logs/screenshots/.gitkeep

diff --git a/.gitignore b/.gitignore
index e1bddf03..3732e540 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,17 @@ nginx/ssl/keys/*
 !**/.gitkeep
 **/node_modules
 **/junit.xml
+
+# Screenshots
+logs/screenshots/*
+!logs/screenshots/.gitkeep
+
+# Fish shell
+$HOME
+
+# JetBrains IDEs
+.idea
+
 # Created by https://www.toptal.com/developers/gitignore/api/intellij,python,flask,macos
 # Edit at https://www.toptal.com/developers/gitignore?templates=intellij,python,flask,macos
 
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index 4f4e9dd3..5da2716d 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -3,6 +3,7 @@
 
 from bci.browser.configuration.browser import Browser as BrowserConfig
 from bci.browser.interaction.simulation import Simulation
+from bci.evaluations.logic import TestParameters
 
 logger = logging.getLogger(__name__)
 
@@ -10,23 +11,21 @@
 class Interaction:
     browser: BrowserConfig
     script: list[str]
+    params: TestParameters
 
-    def __init__(self, browser: BrowserConfig, script: list[str]) -> None:
+    def __init__(self, browser: BrowserConfig, script: list[str], params: TestParameters) -> None:
         self.browser = browser
         self.script = script
+        self.params = params
 
     def execute(self) -> None:
-        simulation = self._initiate_simulation()
+        simulation = Simulation(self.browser, self.params)
 
         self._interpret(simulation)
 
         simulation.navigate('https://a.test/report/?bughog_sanity_check=OK')
         simulation.sleep('0.5')
 
-    def _initiate_simulation(self) -> Simulation:
-        # TODO - possibly return different browser instances
-        return Simulation(self.browser)
-
     def _interpret(self, simulation: Simulation) -> None:
         for statement in self.script:
             if statement.strip() == '':
diff --git a/bci/browser/interaction/simulation.py b/bci/browser/interaction/simulation.py
index 8548d2cf..da22069f 100644
--- a/bci/browser/interaction/simulation.py
+++ b/bci/browser/interaction/simulation.py
@@ -1,6 +1,4 @@
-import base64
 import os
-from io import BytesIO
 from time import sleep
 
 import pyautogui as gui
@@ -8,14 +6,18 @@
 from pyvirtualdisplay.display import Display
 
 from bci.browser.configuration.browser import Browser as BrowserConfig
+from bci.evaluations.logic import TestParameters
 
 
 class Simulation:
     browser_config: BrowserConfig
+    params: TestParameters
+
     public_methods: list[str] = ['navigate', 'click', 'click_el', 'sleep', 'screenshot']
 
-    def __init__(self, browser_config: BrowserConfig):
+    def __init__(self, browser_config: BrowserConfig, params: TestParameters):
         self.browser_config = browser_config
+        self.params = params
         disp = Display(visible=True, size=(1920, 1080), backend='xvfb', use_xauth=True)
         disp.start()
         gui._pyautogui_x11._display = Xlib.display.Display(os.environ['DISPLAY'])
@@ -50,9 +52,7 @@ def click_el(self, el_id: str):
     def sleep(self, duration: str):
         sleep(float(duration))
 
-    def screenshot(self):
-        # TODO save to the filesystem
-        buffered = BytesIO()
-        print(gui.screenshot().save(buffered, format='JPEG'))
-        img_str = base64.b64encode(buffered.getvalue())
-        print(img_str.decode('utf-8'))
+    def screenshot(self, filename: str):
+        filename = f'{self.params.evaluation_configuration.project}-{self.params.mech_group}-{filename}-{type(self.browser_config).__name__}-{self.browser_config.version}.jpg'
+        filepath = os.path.join(os.path.dirname(os.path.realpath(__file__)), '../../../logs/screenshots', filename)
+        gui.screenshot(filepath)
diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index 8e81ed90..3586d7e7 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -105,7 +105,7 @@ def perform_specific_evaluation(self, browser: Browser, params: TestParameters)
 
             max_tries = 3
             if 'interaction_script' in experiment:
-                interaction = Interaction(browser, experiment['interaction_script'])
+                interaction = Interaction(browser, experiment['interaction_script'], params)
                 tries = 0
                 while tries < max_tries:
                     tries += 1
diff --git a/experiments/pages/Support/AutoGUI/a.test/main/index.html b/experiments/pages/Support/AutoGUI/a.test/main/index.html
index f7700d53..fabffa1b 100644
--- a/experiments/pages/Support/AutoGUI/a.test/main/index.html
+++ b/experiments/pages/Support/AutoGUI/a.test/main/index.html
@@ -59,4 +59,4 @@
     left: 45px;
 }
 </style>
-<a href="https://a.test/report/?leak=AutoGUI" class="fullscreen">CLICK</a>
\ No newline at end of file
+<a href="https://a.test/report/?leak=AutoGUI" id="three">CLICK</a>
\ No newline at end of file
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/interaction_script.cmd
index f98842c0..895572c5 100644
--- a/experiments/pages/Support/AutoGUI/interaction_script.cmd
+++ b/experiments/pages/Support/AutoGUI/interaction_script.cmd
@@ -1,8 +1,5 @@
 NAVIGATE https://a.test/Support/AutoGUI/main
 SLEEP 1
-
-SCREENSHOT
-
-# test
-CLICK 200 50%
+SCREENSHOT testtest
+CLICK_EL three
 SLEEP 1
\ No newline at end of file
diff --git a/logs/screenshots/.gitkeep b/logs/screenshots/.gitkeep
new file mode 100644
index 00000000..e69de29b

From 63ab107c168d5b482c0e628e440d49de9eb740d8 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 09:10:46 +0000
Subject: [PATCH 26/57] Fix collector notifications status code

---
 nginx/config/experiments.conf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nginx/config/experiments.conf b/nginx/config/experiments.conf
index 398dac9c..1ecb90be 100644
--- a/nginx/config/experiments.conf
+++ b/nginx/config/experiments.conf
@@ -2,7 +2,7 @@ access_log /logs/nginx-access-poc.log default_format;
 
 location /res/ {
     include /etc/nginx/config/notify_collector.conf;
-    error_page 504 @resources;
+    error_page 504 =200 @resources;
 }
 
 location @resources {
@@ -62,7 +62,7 @@ location ~ ^/(.+)/(.+)/(.+)/$ {
 
 location ~ ^/(.+)/(.+)/(.+)$ {
     include /etc/nginx/config/notify_collector.conf;
-    error_page 504 @experiment;
+    error_page 504 =200 @experiment;
 }
 
 location @experiment {

From dcbc707b4e27c55709b2ed5c40f42254c176ac46 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 09:10:57 +0000
Subject: [PATCH 27/57] Remove redundant styles

---
 .../Support/AutoGUI/a.test/main/index.html    | 60 -------------------
 1 file changed, 60 deletions(-)

diff --git a/experiments/pages/Support/AutoGUI/a.test/main/index.html b/experiments/pages/Support/AutoGUI/a.test/main/index.html
index fabffa1b..c26ef023 100644
--- a/experiments/pages/Support/AutoGUI/a.test/main/index.html
+++ b/experiments/pages/Support/AutoGUI/a.test/main/index.html
@@ -1,62 +1,2 @@
 <link rel="stylesheet" href="https://a.test/res/bughog.css">
-<style>
-.fullscreen {
-    position: fixed;
-    top: 0;
-    left: 0;
-    width: 100%;
-    height: 100%;
-    background-color: red;
-    z-index: 10;
-}
-
-#one, #two, #three, #four, #five, #six {
-    position: fixed;
-    width: 25px;
-    height: 20px;
-    font-size: 0;
-}
-
-#one {
-    background-color: #800000;
-    color: #800000;
-    top: 10px;
-    left: 10px;
-}
-
-#two {
-    background-color: #dcbeff;
-    color: #dcbeff;
-    top: 45px;
-    left: 10px;
-}
-
-#three {
-    background-color: #ffe119;
-    color: #ffe119;
-    top: 80px;
-    left: 10px;
-}
-
-#four {
-    background-color: #4363d8;
-    color: #4363d8;
-    top: 10px;
-    left: 45px;
-}
-
-#five {
-    background-color: #f58231;
-    color: #f58231;
-    top: 45px;
-    left: 45px;
-}
-
-#six {
-    background-color: #000075;
-    color: #000075;
-    top: 80px;
-    left: 45px;
-}
-</style>
 <a href="https://a.test/report/?leak=AutoGUI" id="three">CLICK</a>
\ No newline at end of file

From 2fc829b565af2c6e5f607be5526e074a77670c25 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 09:30:10 +0000
Subject: [PATCH 28/57] Add default experiment file values

---
 bci/evaluations/custom/custom_evaluation.py   | 23 +++++--------------
 .../custom/default_files/headers.json         |  6 +++++
 bci/evaluations/custom/default_files/html     | 10 ++++++++
 .../default_files/interaction_script.cmd      |  7 ++++++
 bci/evaluations/custom/default_files/js       |  1 +
 bci/evaluations/custom/default_files/py       | 15 ++++++++++++
 .../custom/default_files/url_queue.txt        |  2 ++
 7 files changed, 47 insertions(+), 17 deletions(-)
 create mode 100644 bci/evaluations/custom/default_files/headers.json
 create mode 100644 bci/evaluations/custom/default_files/html
 create mode 100644 bci/evaluations/custom/default_files/interaction_script.cmd
 create mode 100644 bci/evaluations/custom/default_files/js
 create mode 100644 bci/evaluations/custom/default_files/py
 create mode 100644 bci/evaluations/custom/default_files/url_queue.txt

diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index 3586d7e7..84517c9c 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -202,18 +202,7 @@ def add_page(self, project: str, poc: str, domain: str, path: str, file_type: st
             headers_file_path = os.path.join(page_path, 'headers.json')
             if not os.path.exists(headers_file_path):
                 with open(headers_file_path, 'w') as file:
-                    file.write(
-                        textwrap.dedent(
-                            """\
-                            [
-                                {
-                                    "key": "Header-Name",
-                                    "value": "Header-Value"
-                                }
-                            ]
-                        """
-                        )
-                    )
+                    file.write(self.get_default_file_content('headers.json'))
         self.sync_with_folders()
         # Notify clients of change (an experiment might now be runnable)
         Clients.push_experiments_to_all()
@@ -221,13 +210,13 @@ def add_page(self, project: str, poc: str, domain: str, path: str, file_type: st
 
     @staticmethod
     def get_default_file_content(file_type: str) -> str:
-        if file_type != 'py':
-            return ''
+        path = os.path.join(os.path.dirname(os.path.realpath(__file__)), f'default_files/{file_type}')
 
-        with open('experiments/pages/Support/PythonServer/a.test/py-server/index.py', 'r') as file:
-            template_content = file.read()
+        if not os.path.exists(path):
+            return ''
 
-        return template_content
+        with open(path, 'r') as file:
+            return file.read()
 
     @staticmethod
     def include_file_headers(file_type: str) -> bool:
diff --git a/bci/evaluations/custom/default_files/headers.json b/bci/evaluations/custom/default_files/headers.json
new file mode 100644
index 00000000..81975b3f
--- /dev/null
+++ b/bci/evaluations/custom/default_files/headers.json
@@ -0,0 +1,6 @@
+[
+    {
+        "key": "Header-Name",
+        "value": "Header-Value"
+    }
+]
\ No newline at end of file
diff --git a/bci/evaluations/custom/default_files/html b/bci/evaluations/custom/default_files/html
new file mode 100644
index 00000000..2af82326
--- /dev/null
+++ b/bci/evaluations/custom/default_files/html
@@ -0,0 +1,10 @@
+<!DOCTYPE html>
+<html>
+<head>
+    <link rel="stylesheet" href="/res/bughog.css">
+    <script src="/res/bughog.js"></script>
+</head>
+<body>
+    <!-- TODO - implement your PoC -->
+</body>
+</html>
\ No newline at end of file
diff --git a/bci/evaluations/custom/default_files/interaction_script.cmd b/bci/evaluations/custom/default_files/interaction_script.cmd
new file mode 100644
index 00000000..59f6d22b
--- /dev/null
+++ b/bci/evaluations/custom/default_files/interaction_script.cmd
@@ -0,0 +1,7 @@
+# TODO - add your interaction script
+
+# NAVIGATE https://a.test/Project/Experiment/main
+# SLEEP 1
+# SCREENSHOT file_name
+# CLICK_EL one
+# SLEEP 1
\ No newline at end of file
diff --git a/bci/evaluations/custom/default_files/js b/bci/evaluations/custom/default_files/js
new file mode 100644
index 00000000..664997c1
--- /dev/null
+++ b/bci/evaluations/custom/default_files/js
@@ -0,0 +1 @@
+// TODO - implement your PoC
\ No newline at end of file
diff --git a/bci/evaluations/custom/default_files/py b/bci/evaluations/custom/default_files/py
new file mode 100644
index 00000000..91e823b8
--- /dev/null
+++ b/bci/evaluations/custom/default_files/py
@@ -0,0 +1,15 @@
+from flask import Request
+
+# Make sure that your page directory starts with 'py-'
+
+def main(req: Request):
+    # TODO - implement your functionality and return a Flask response
+    
+    return {
+        "agent": req.headers.get("User-Agent"),
+        "cookies": req.cookies,
+        "host": req.host,
+        "path": req.path,
+        "scheme": req.scheme,
+        "url": req.url
+    }
\ No newline at end of file
diff --git a/bci/evaluations/custom/default_files/url_queue.txt b/bci/evaluations/custom/default_files/url_queue.txt
new file mode 100644
index 00000000..8918d8d1
--- /dev/null
+++ b/bci/evaluations/custom/default_files/url_queue.txt
@@ -0,0 +1,2 @@
+TODO - add your URLs to visit
+https://a.test/report/?bughog_sanity_check=OK
\ No newline at end of file

From 5fbb38b5e48c77d9ddb9896654f723d2c1f0e312 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 09:30:20 +0000
Subject: [PATCH 29/57] Refactor experiment

---
 .../pages/Support/AutoGUI/a.test/main/index.html     | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/experiments/pages/Support/AutoGUI/a.test/main/index.html b/experiments/pages/Support/AutoGUI/a.test/main/index.html
index c26ef023..70d626e3 100644
--- a/experiments/pages/Support/AutoGUI/a.test/main/index.html
+++ b/experiments/pages/Support/AutoGUI/a.test/main/index.html
@@ -1,2 +1,10 @@
-<link rel="stylesheet" href="https://a.test/res/bughog.css">
-<a href="https://a.test/report/?leak=AutoGUI" id="three">CLICK</a>
\ No newline at end of file
+<!DOCTYPE html>
+<html>
+<head>
+    <link rel="stylesheet" href="/res/bughog.css">
+    <script src="/res/bughog.js"></script>
+</head>
+<body>
+    <a href="/report/?leak=AutoGUI" id="three">CLICK</a>
+</body>
+</html>
\ No newline at end of file

From 6e366bda88527d21aa121bdb32a57c971600d36a Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 09:41:10 +0000
Subject: [PATCH 30/57] Better selectors styling

---
 experiments/res/bughog.css | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/experiments/res/bughog.css b/experiments/res/bughog.css
index 10be4b2d..7cdbfa7d 100644
--- a/experiments/res/bughog.css
+++ b/experiments/res/bughog.css
@@ -1,18 +1,23 @@
-.fullscreen {
+#fullscreen, #one, #two, #three, #four, #five, #six {
     position: fixed;
+    z-index: 10;
+    font-size: 0;
+    border: none;
+    outline: none;
+    resize: none;
+}
+
+#fullscreen {
     top: 0;
     left: 0;
     width: 100%;
     height: 100%;
     background-color: red;
-    z-index: 10;
 }
 
 #one, #two, #three, #four, #five, #six {
-    position: fixed;
     width: 25px;
     height: 20px;
-    font-size: 0;
 }
 
 #one {

From 45710c2ac3ed21536fd293cdf7e22183b059ec5a Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 10:33:16 +0000
Subject: [PATCH 31/57] Adding config files through the frontend - Vue part

---
 bci/web/vue/src/components/poc-editor.vue | 55 ++++++++++++++++++++---
 bci/web/vue/src/main.js                   |  4 +-
 bci/web/vue/src/style.css                 |  8 ++--
 3 files changed, 55 insertions(+), 12 deletions(-)

diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 48253620..78d2f526 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -46,6 +46,10 @@
           'js',
           'py',
         ],
+        available_config_types: {
+          'interaction_script': 'Interaction script',
+          'url_queue': 'URL queue'
+        },
         poc_tree_config: {
           domain: 'Config',
           page: '_',
@@ -61,12 +65,16 @@
             type: null,
           }
         },
+        config_type: null,
         editor: null,
         timeout: null,
       }
     },
     computed: {
       active_poc_tree() {
+        const configDomain = this.poc_tree_config.domain;
+        const configPage = this.poc_tree_config.page;
+
         return Object.entries(this.active_poc.tree).reduce((acc, [domain, pages]) => {
           if (domain !== pages) {
             return [
@@ -75,11 +83,8 @@
             ]
           }
 
-          const configDomain = this.poc_tree_config.domain;
-          const configPage = this.poc_tree_config.page;
-
           // A single top-level file -> create a virtual config folder
-          const config_folder = acc.find(([domain]) => domain === configDomain) ?? [configDomain, {[configPage]: {}}];
+          const config_folder = acc.find(([domain]) => domain === configDomain);
           return [
             ...acc.filter(([domain]) => domain !== configDomain),
             [configDomain, {
@@ -89,7 +94,7 @@
               }
             }],
           ]
-        }, []);
+        }, [[configDomain, {[configPage]: {}}]]);
       }
     },
     methods: {
@@ -198,6 +203,19 @@
         })
         .catch(() => {
 
+        });
+      },
+      add_config() {
+        const url = `/api/poc/${this.project}/${this.poc}/config`;
+        axios.post(url, {
+          "type": this.config_type,
+        })
+        .then(() => {
+          this.update_poc_tree();
+          this.config_type = null;
+        })
+        .catch(() => {
+
         });
       }
     },
@@ -248,7 +266,12 @@
                     </a>
                   </template>
                   <template v-else>
-                    {{ domain}}
+                    <div class="w-full">
+                      {{ domain}}
+                    </div>
+                    <button v-if="files && Object.keys(files).length === 0" class="no-style" onclick="create_config_dialog.showModal()">
+                      <v-icon name="fa-plus" class="text-indigo-500"/>
+                    </button>
                   </template>
                 </div>
                 <ul>
@@ -304,4 +327,24 @@
       </div>
     </form>
   </dialog>
+
+  <!-- Create config dialog -->
+  <dialog id="create_config_dialog" class="dialog">
+    <form method="dialog" @submit="add_config">
+      <p>
+        <label>
+          <div class="py-2">Choose config type:</div>
+          <select name="config_type" id="config_type" v-model="config_type" required>
+            <option v-for="(label, value) of available_config_types" :value="value">
+              {{ label }}
+            </option>
+          </select>
+        </label>
+      </p>
+      <div class="flex pt-3">
+        <input class="button m-2 w-full" type="submit" value="Create config">
+        <input class="button m-2" type="button" value="Cancel" onclick="create_config_dialog.close()">
+      </div>
+    </form>
+  </dialog>
 </template>
diff --git a/bci/web/vue/src/main.js b/bci/web/vue/src/main.js
index 70ff98b0..121570e3 100644
--- a/bci/web/vue/src/main.js
+++ b/bci/web/vue/src/main.js
@@ -5,8 +5,8 @@ import 'flowbite'
 import 'axios'
 
 import { OhVueIcon, addIcons } from "oh-vue-icons";
-import { MdInfooutline, FaRegularEdit, FaLink } from "oh-vue-icons/icons";
+import { MdInfooutline, FaRegularEdit, FaLink, FaPlus } from "oh-vue-icons/icons";
 
-addIcons(MdInfooutline, FaRegularEdit, FaLink);
+addIcons(MdInfooutline, FaRegularEdit, FaLink, FaPlus);
 const app = createApp(App);
 app.component("v-icon", OhVueIcon).mount('#app')
diff --git a/bci/web/vue/src/style.css b/bci/web/vue/src/style.css
index 713de6c3..12c7eb4c 100644
--- a/bci/web/vue/src/style.css
+++ b/bci/web/vue/src/style.css
@@ -3,7 +3,7 @@
 @tailwind utilities;
 
 .button {
-  @apply text-white bg-blue-700 hover:bg-blue-800 active:ring-4 focus:outline-none font-medium rounded-lg text-sm px-4 py-2.5 text-center items-center dark:hover:bg-blue-700 dark:focus:ring-blue-800
+  @apply text-white bg-blue-700 hover:bg-blue-800 active:ring-4 focus:outline-none cursor-pointer font-medium rounded-lg text-sm px-4 py-2.5 text-center items-center dark:hover:bg-blue-700 dark:focus:ring-blue-800
 }
 
 .dropdown-head {
@@ -192,7 +192,7 @@ h1 {
   line-height: 1.1;
 }
 
-button {
+button:not(.no-style) {
   border-radius: 8px;
   border: 1px solid transparent;
   padding: 0.6em 1.2em;
@@ -203,8 +203,8 @@ button {
   cursor: pointer;
   transition: border-color 0.25s;
 }
-button:focus,
-button:focus-visible {
+button:not(.no-style):focus,
+button:not(.no-style):focus-visible {
   outline: 4px auto -webkit-focus-ring-color;
 }
 

From acdec3cf51e5c1e4b5f5e2dfc2993b924767789e Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 10:42:29 +0000
Subject: [PATCH 32/57] Adding config files through the frontend - Python part

---
 bci/evaluations/custom/custom_evaluation.py | 16 ++++++++++++++++
 bci/main.py                                 |  4 ++++
 bci/web/blueprints/api.py                   | 14 ++++++++++++++
 bci/web/vue/src/components/poc-editor.vue   |  4 ++--
 4 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index 84517c9c..baa464a3 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -207,6 +207,22 @@ def add_page(self, project: str, poc: str, domain: str, path: str, file_type: st
         # Notify clients of change (an experiment might now be runnable)
         Clients.push_experiments_to_all()
         return True
+    
+    def add_config(self, project: str, poc: str, type: str) -> bool:
+        content = self.get_default_file_content(type)
+
+        if (content == ''):
+            return False
+
+        file_path = os.path.join(Global.custom_page_folder, project, poc, type)
+        with open(file_path, 'w') as file:
+            file.write(content)
+        
+        self.sync_with_folders()
+        # Notify clients of change (an experiment might now be runnable)
+        Clients.push_experiments_to_all()
+
+        return True
 
     @staticmethod
     def get_default_file_content(file_type: str) -> str:
diff --git a/bci/main.py b/bci/main.py
index 127c1c29..fddb53ae 100644
--- a/bci/main.py
+++ b/bci/main.py
@@ -155,6 +155,10 @@ def get_available_domains() -> list[str]:
     @staticmethod
     def add_page(project: str, poc: str, domain: str, path: str, file_type: str) -> bool:
         return Main.master.evaluation_framework.add_page(project, poc, domain, path, file_type)
+    
+    @staticmethod
+    def add_config(project: str, poc: str, type: str) -> bool:
+        return Main.master.evaluation_framework.add_config(project, poc, type)
 
     @staticmethod
     def sigint_handler(signum, frame):
diff --git a/bci/web/blueprints/api.py b/bci/web/blueprints/api.py
index 592fbcab..8c1094b8 100644
--- a/bci/web/blueprints/api.py
+++ b/bci/web/blueprints/api.py
@@ -208,6 +208,20 @@ def add_page(project: str, poc: str):
         }
 
 
+@api.route('/poc/<string:project>/<string:poc>/config', methods=['POST'])
+def add_config(project: str, poc: str):
+    data = request.json.copy()
+    success = bci_api.add_config(project, poc, data['type'])
+    if success:
+        return {
+            'status': 'OK'
+        }
+    else:
+        return {
+            'status': 'NOK'
+        }
+
+
 @api.route('/poc/domain/', methods=['GET'])
 def get_available_domains():
     return {
diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 78d2f526..45cffbed 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -47,8 +47,8 @@
           'py',
         ],
         available_config_types: {
-          'interaction_script': 'Interaction script',
-          'url_queue': 'URL queue'
+          'interaction_script.cmd': 'Interaction script',
+          'url_queue.txt': 'URL queue'
         },
         poc_tree_config: {
           domain: 'Config',

From 3ee4d20e19d748bcd2210b846966e8ea1deb6516 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 12:06:47 +0000
Subject: [PATCH 33/57] More interaction commands

---
 bci/browser/interaction/interaction.py        | 14 ++++----
 bci/browser/interaction/simulation.py         | 35 ++++++++++++++++---
 .../default_files/interaction_script.cmd      | 17 +++++----
 bci/web/vue/src/interaction_script_mode.js    |  2 +-
 .../Support/AutoGUI/a.test/main/index.html    |  6 +++-
 .../Support/AutoGUI/interaction_script.cmd    | 19 ++++++++--
 experiments/res/bughog.css                    |  2 +-
 7 files changed, 71 insertions(+), 24 deletions(-)

diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index 5da2716d..4561fff5 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -22,32 +22,30 @@ def execute(self) -> None:
         simulation = Simulation(self.browser, self.params)
 
         self._interpret(simulation)
+        simulation.sleep('0.5')
 
         simulation.navigate('https://a.test/report/?bughog_sanity_check=OK')
-        simulation.sleep('0.5')
 
     def _interpret(self, simulation: Simulation) -> None:
         for statement in self.script:
-            if statement.strip() == '':
+            if statement.strip() == '' or statement[0] == '#':
                 continue
 
             cmd, *args = statement.split()
             method_name = cmd.lower()
 
-            if cmd == '#':
-                continue
-
             if method_name not in Simulation.public_methods:
                 raise Exception(
                     f'Invalid command `{cmd}`. Expected one of {", ".join(map(lambda m: m.upper(), Simulation.public_methods))}.'
                 )
 
             method = getattr(simulation, method_name)
-            method_params_len = len(signature(method).parameters)
+            method_params = list(signature(method).parameters.values())
 
-            if method_params_len != len(args):
+            # Allow different number of arguments only for variable argument number (*)
+            if len(method_params) != len(args) and (len(method_params) < 1 or str(method_params[0])[0] != '*'):
                 raise Exception(
-                    f'Invalid number of arguments for command `{cmd}`. Expected {method_params_len}, got {len(args)}.'
+                    f'Invalid number of arguments for command `{cmd}`. Expected {len(method_params)}, got {len(args)}.'
                 )
 
             logger.debug(f'Executing interaction method `{method_name}` with the arguments {args}')
diff --git a/bci/browser/interaction/simulation.py b/bci/browser/interaction/simulation.py
index da22069f..68da367e 100644
--- a/bci/browser/interaction/simulation.py
+++ b/bci/browser/interaction/simulation.py
@@ -13,7 +13,18 @@ class Simulation:
     browser_config: BrowserConfig
     params: TestParameters
 
-    public_methods: list[str] = ['navigate', 'click', 'click_el', 'sleep', 'screenshot']
+    public_methods: list[str] = [
+        'navigate',
+        'click_position',
+        'click',
+        'write',
+        'press',
+        'hold',
+        'release',
+        'hotkey',
+        'sleep',
+        'screenshot',
+    ]
 
     def __init__(self, browser_config: BrowserConfig, params: TestParameters):
         self.browser_config = browser_config
@@ -37,17 +48,33 @@ def parse_position(self, position: str, max_value: int) -> int:
     def navigate(self, url: str):
         self.browser_config.terminate()
         self.browser_config.open(url)
+        self.sleep('0.5')
 
-    def click(self, x: str, y: str):
+    def click_position(self, x: str, y: str):
         max_x, max_y = gui.size()
 
         gui.moveTo(self.parse_position(x, max_x), self.parse_position(y, max_y))
         gui.click()
 
-    def click_el(self, el_id: str):
+    def click(self, el_id: str):
         el_image_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), f'elements/{el_id}.png')
         x, y = gui.locateCenterOnScreen(el_image_path)
-        self.click(str(x), str(y))
+        self.click_position(str(x), str(y))
+
+    def write(self, text: str):
+        gui.write(text, interval=0.1)
+
+    def press(self, key: str):
+        gui.press(key)
+
+    def hold(self, key: str):
+        gui.keyDown(key)
+
+    def release(self, key: str):
+        gui.keyUp(key)
+
+    def hotkey(self, *keys: str):
+        gui.hotkey(*keys)
 
     def sleep(self, duration: str):
         sleep(float(duration))
diff --git a/bci/evaluations/custom/default_files/interaction_script.cmd b/bci/evaluations/custom/default_files/interaction_script.cmd
index 59f6d22b..63ad6d9b 100644
--- a/bci/evaluations/custom/default_files/interaction_script.cmd
+++ b/bci/evaluations/custom/default_files/interaction_script.cmd
@@ -1,7 +1,12 @@
-# TODO - add your interaction script
+# TODO - add your interaction script using the commands 
 
-# NAVIGATE https://a.test/Project/Experiment/main
-# SLEEP 1
-# SCREENSHOT file_name
-# CLICK_EL one
-# SLEEP 1
\ No newline at end of file
+# NAVIGATE url
+# CLICK_POSITION x y    where x and y are absolute numbers or screen percentages
+# CLICK element_id      where element_id is one of one, two, three, four, five, six
+# WRITE text
+# PRESS key
+# HOLD key
+# RELEASE key
+# HOTKEY key1 key2 ...
+# SLEEP seconds         where seconds is a float or an int
+# SCREENSHOT file_name
\ No newline at end of file
diff --git a/bci/web/vue/src/interaction_script_mode.js b/bci/web/vue/src/interaction_script_mode.js
index 35785b44..4413d521 100644
--- a/bci/web/vue/src/interaction_script_mode.js
+++ b/bci/web/vue/src/interaction_script_mode.js
@@ -1,4 +1,4 @@
-const KEYWORDS = "NAVIGATE|CLICK|CLICK_EL|SLEEP|SCREENSHOT";
+const KEYWORDS = "NAVIGATE|CLICK_POSITION|CLICK|WRITE|PRESS|HOLD|RELEASE|HOTKEY|SLEEP|SCREENSHOT";
 
 ace.define("ace/mode/interaction_script_highlight_rules",["require","exports","module","ace/lib/oop","ace/mode/text_highlight_rules"], function(require, exports, module){"use strict";
     const oop = require("../lib/oop");
diff --git a/experiments/pages/Support/AutoGUI/a.test/main/index.html b/experiments/pages/Support/AutoGUI/a.test/main/index.html
index 70d626e3..e2b6d3c4 100644
--- a/experiments/pages/Support/AutoGUI/a.test/main/index.html
+++ b/experiments/pages/Support/AutoGUI/a.test/main/index.html
@@ -5,6 +5,10 @@
     <script src="/res/bughog.js"></script>
 </head>
 <body>
-    <a href="/report/?leak=AutoGUI" id="three">CLICK</a>
+    <form action="/report" method="GET">
+        <input id="one">
+        <input name="leak" id="two">
+        <input type="submit">
+    </form>
 </body>
 </html>
\ No newline at end of file
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/interaction_script.cmd
index 895572c5..a9ed5d45 100644
--- a/experiments/pages/Support/AutoGUI/interaction_script.cmd
+++ b/experiments/pages/Support/AutoGUI/interaction_script.cmd
@@ -1,5 +1,18 @@
 NAVIGATE https://a.test/Support/AutoGUI/main
 SLEEP 1
-SCREENSHOT testtest
-CLICK_EL three
-SLEEP 1
\ No newline at end of file
+SCREENSHOT test
+
+CLICK one
+WRITE AutoGUI
+HOTKEY ctrl a
+HOTKEY ctrl c
+
+CLICK two
+
+# Equivalent to HOTKEY ctrl v
+HOLD ctrl
+HOLD v
+RELEASE v
+RELEASE ctrl
+
+PRESS Enter
\ No newline at end of file
diff --git a/experiments/res/bughog.css b/experiments/res/bughog.css
index 7cdbfa7d..fd01d4cd 100644
--- a/experiments/res/bughog.css
+++ b/experiments/res/bughog.css
@@ -1,7 +1,7 @@
 #fullscreen, #one, #two, #three, #four, #five, #six {
     position: fixed;
     z-index: 10;
-    font-size: 0;
+    font-size: 1px;
     border: none;
     outline: none;
     resize: none;

From 52211d03ee147b2f08f5a2f9a1ef7f0aae177fff Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 12:11:14 +0000
Subject: [PATCH 34/57] Styling fix

---
 bci/web/vue/src/style.css | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/bci/web/vue/src/style.css b/bci/web/vue/src/style.css
index 12c7eb4c..c52649c6 100644
--- a/bci/web/vue/src/style.css
+++ b/bci/web/vue/src/style.css
@@ -192,7 +192,7 @@ h1 {
   line-height: 1.1;
 }
 
-button:not(.no-style) {
+button {
   border-radius: 8px;
   border: 1px solid transparent;
   padding: 0.6em 1.2em;
@@ -203,11 +203,17 @@ button:not(.no-style) {
   cursor: pointer;
   transition: border-color 0.25s;
 }
-button:not(.no-style):focus,
-button:not(.no-style):focus-visible {
+button:focus,
+button:focus-visible {
   outline: 4px auto -webkit-focus-ring-color;
 }
 
+button.no-style {
+  padding: 0;
+  background: transparent;
+  border: none;
+}
+
 .card {
   padding: 2em;
 }

From 639441c6c4d7144609a2568ed759751f25d3ccb8 Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 13:25:22 +0000
Subject: [PATCH 35/57] Final interaction improvements

---
 bci/browser/configuration/browser.py            |  4 ++++
 bci/browser/configuration/chromium.py           |  3 +++
 bci/browser/configuration/firefox.py            |  3 +++
 bci/browser/interaction/interaction.py          | 17 +++++++++++------
 bci/browser/interaction/simulation.py           |  2 +-
 .../Support/AutoGUI/a.test/main/index.html      |  2 +-
 .../Support/AutoGUI/interaction_script.cmd      |  4 ++--
 experiments/res/bughog.css                      | 14 +++++++-------
 8 files changed, 32 insertions(+), 17 deletions(-)

diff --git a/bci/browser/configuration/browser.py b/bci/browser/configuration/browser.py
index 0247f28e..f6a9f2e7 100644
--- a/bci/browser/configuration/browser.py
+++ b/bci/browser/configuration/browser.py
@@ -100,6 +100,10 @@ def _get_executable_file_path(self) -> str:
     def _get_terminal_args(self) -> list[str]:
         pass
 
+    @abstractmethod
+    def get_navigation_sleep_duration(self) -> int:
+        pass
+
     @staticmethod
     def get_browser(
         browser_config: BrowserConfiguration, eval_config: EvaluationConfiguration, state: State
diff --git a/bci/browser/configuration/chromium.py b/bci/browser/configuration/chromium.py
index 6108328d..f2cd16cb 100644
--- a/bci/browser/configuration/chromium.py
+++ b/bci/browser/configuration/chromium.py
@@ -32,6 +32,9 @@
 
 class Chromium(Browser):
 
+    def get_navigation_sleep_duration(self) -> int:
+        return 1
+
     def _get_terminal_args(self) -> list[str]:
         assert self._profile_path is not None
 
diff --git a/bci/browser/configuration/firefox.py b/bci/browser/configuration/firefox.py
index 4310bf20..cff1d7f1 100644
--- a/bci/browser/configuration/firefox.py
+++ b/bci/browser/configuration/firefox.py
@@ -20,6 +20,9 @@
 
 class Firefox(Browser):
 
+    def get_navigation_sleep_duration(self) -> int:
+        return 2
+
     def _get_terminal_args(self) -> list[str]:
         assert self._profile_path is not None
 
diff --git a/bci/browser/interaction/interaction.py b/bci/browser/interaction/interaction.py
index 4561fff5..14fb8d1b 100644
--- a/bci/browser/interaction/interaction.py
+++ b/bci/browser/interaction/interaction.py
@@ -21,12 +21,11 @@ def __init__(self, browser: BrowserConfig, script: list[str], params: TestParame
     def execute(self) -> None:
         simulation = Simulation(self.browser, self.params)
 
-        self._interpret(simulation)
-        simulation.sleep('0.5')
+        if self._interpret(simulation):
+            simulation.sleep(str(self.browser.get_navigation_sleep_duration()))
+            simulation.navigate('https://a.test/report/?bughog_sanity_check=OK')
 
-        simulation.navigate('https://a.test/report/?bughog_sanity_check=OK')
-
-    def _interpret(self, simulation: Simulation) -> None:
+    def _interpret(self, simulation: Simulation) -> bool:
         for statement in self.script:
             if statement.strip() == '' or statement[0] == '#':
                 continue
@@ -49,4 +48,10 @@ def _interpret(self, simulation: Simulation) -> None:
                 )
 
             logger.debug(f'Executing interaction method `{method_name}` with the arguments {args}')
-            method(*args)
+
+            try:
+                method(*args)
+            except:
+                return False
+
+        return True
diff --git a/bci/browser/interaction/simulation.py b/bci/browser/interaction/simulation.py
index 68da367e..d4ba899c 100644
--- a/bci/browser/interaction/simulation.py
+++ b/bci/browser/interaction/simulation.py
@@ -48,7 +48,7 @@ def parse_position(self, position: str, max_value: int) -> int:
     def navigate(self, url: str):
         self.browser_config.terminate()
         self.browser_config.open(url)
-        self.sleep('0.5')
+        self.sleep(str(self.browser_config.get_navigation_sleep_duration()))
 
     def click_position(self, x: str, y: str):
         max_x, max_y = gui.size()
diff --git a/experiments/pages/Support/AutoGUI/a.test/main/index.html b/experiments/pages/Support/AutoGUI/a.test/main/index.html
index e2b6d3c4..93eb4fc7 100644
--- a/experiments/pages/Support/AutoGUI/a.test/main/index.html
+++ b/experiments/pages/Support/AutoGUI/a.test/main/index.html
@@ -5,7 +5,7 @@
     <script src="/res/bughog.js"></script>
 </head>
 <body>
-    <form action="/report" method="GET">
+    <form action="/report/" method="GET">
         <input id="one">
         <input name="leak" id="two">
         <input type="submit">
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/interaction_script.cmd
index a9ed5d45..91d6f21f 100644
--- a/experiments/pages/Support/AutoGUI/interaction_script.cmd
+++ b/experiments/pages/Support/AutoGUI/interaction_script.cmd
@@ -1,12 +1,12 @@
 NAVIGATE https://a.test/Support/AutoGUI/main
-SLEEP 1
-SCREENSHOT test
 
+SCREENSHOT click1
 CLICK one
 WRITE AutoGUI
 HOTKEY ctrl a
 HOTKEY ctrl c
 
+SCREENSHOT click2
 CLICK two
 
 # Equivalent to HOTKEY ctrl v
diff --git a/experiments/res/bughog.css b/experiments/res/bughog.css
index fd01d4cd..8fe70435 100644
--- a/experiments/res/bughog.css
+++ b/experiments/res/bughog.css
@@ -30,14 +30,14 @@
 #two {
     background-color: #dcbeff;
     color: #dcbeff;
-    top: 45px;
+    top: 70px;
     left: 10px;
 }
 
 #three {
     background-color: #ffe119;
     color: #ffe119;
-    top: 80px;
+    top: 130px;
     left: 10px;
 }
 
@@ -45,19 +45,19 @@
     background-color: #4363d8;
     color: #4363d8;
     top: 10px;
-    left: 45px;
+    left: 85px;
 }
 
 #five {
     background-color: #f58231;
     color: #f58231;
-    top: 45px;
-    left: 45px;
+    top: 70px;
+    left: 85px;
 }
 
 #six {
     background-color: #000075;
     color: #000075;
-    top: 80px;
-    left: 45px;
+    top: 130px;
+    left: 85px;
 }
\ No newline at end of file

From 8e4af952e4915460c239a95e450b4060087f255d Mon Sep 17 00:00:00 2001
From: Jakub Szymsza <jakub@szymsza.cz>
Date: Fri, 1 Nov 2024 13:29:05 +0000
Subject: [PATCH 36/57] Remove old experiment

---
 .../pages/Support/UserInteraction/a.test/main/headers.json  | 1 -
 .../pages/Support/UserInteraction/a.test/main/index.html    | 6 ------
 .../pages/Support/UserInteraction/interaction_script.cmd    | 1 -
 3 files changed, 8 deletions(-)
 delete mode 100644 experiments/pages/Support/UserInteraction/a.test/main/headers.json
 delete mode 100644 experiments/pages/Support/UserInteraction/a.test/main/index.html
 delete mode 100644 experiments/pages/Support/UserInteraction/interaction_script.cmd

diff --git a/experiments/pages/Support/UserInteraction/a.test/main/headers.json b/experiments/pages/Support/UserInteraction/a.test/main/headers.json
deleted file mode 100644
index fe51488c..00000000
--- a/experiments/pages/Support/UserInteraction/a.test/main/headers.json
+++ /dev/null
@@ -1 +0,0 @@
-[]
diff --git a/experiments/pages/Support/UserInteraction/a.test/main/index.html b/experiments/pages/Support/UserInteraction/a.test/main/index.html
deleted file mode 100644
index ad482c63..00000000
--- a/experiments/pages/Support/UserInteraction/a.test/main/index.html
+++ /dev/null
@@ -1,6 +0,0 @@
-<a href="http://a.test/report/?leak=UserInteraction" style="position: fixed; top: 0; left: 0; width: 100%; height: 100%; background-color: red;" id="leak">
-    CLICK
-</a>
-<script>
-    document.getElementById('leak').click();
-</script>
\ No newline at end of file
diff --git a/experiments/pages/Support/UserInteraction/interaction_script.cmd b/experiments/pages/Support/UserInteraction/interaction_script.cmd
deleted file mode 100644
index 5daa56cf..00000000
--- a/experiments/pages/Support/UserInteraction/interaction_script.cmd
+++ /dev/null
@@ -1 +0,0 @@
-NAVIGATE https://a.test/Support/UserInteraction/main

From a2e61c2b4b1fd2e5de940159b2762fff2929278d Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Wed, 13 Nov 2024 11:17:54 +0000
Subject: [PATCH 37/57] Fix button to add script

---
 bci/web/vue/src/components/poc-editor.vue | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index ff9afb5b..a750fb01 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -232,6 +232,14 @@
         .catch(() => {
 
         });
+      },
+      has_config() {
+        if (this.active_poc.tree === undefined) {
+          console.error("Could not check config in undefined poc tree");
+          return false;
+        }
+        const arr = Object.keys(this.active_poc.tree).filter((domain) => ['url_queue.txt', 'interaction_script.cmd'].includes(domain));
+        return arr.length > 0;
       }
     },
     mounted() {
@@ -292,9 +300,6 @@
                     <a :href="'https://'+domain+'/'+this.project+'/'+this.active_poc.name+'/'+path" target="_blank">
                       <v-icon name="fa-link" class=""/>
                     </a>
-                    <button v-if="files && Object.keys(files).length === 0" class="no-style" onclick="create_config_dialog.showModal()">
-                      <v-icon name="fa-plus" class="text-indigo-500"/>
-                    </button>
                   </div>
                   <ul>
                     <li v-for="([file, _]) in Object.entries(files)"
@@ -328,9 +333,14 @@
               </li>
             </ul>
           </li>
-          <li role="button" class="button text-center" onclick="create_domain_dialog.showModal()">
-            Add page
-          </li>
+          <div class="flex flex-row justify-between">
+            <li role="button" class="button text-center w-full mr-1" onclick="create_domain_dialog.showModal()">
+              Add page
+            </li>
+            <li v-if="!this.has_config()" role="button" class="button text-center w-full mr-1" onclick="create_config_dialog.showModal()">
+              Add script
+            </li>
+          </div>
         </nav>
       </ul>
     </div>

From 792447e4384be3164169f85bc12f35c9b75efe14 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Wed, 13 Nov 2024 12:10:55 +0000
Subject: [PATCH 38/57] Rename interaction_script.cmd to script.md and small
 button fix

---
 bci/evaluations/custom/custom_evaluation.py   | 10 ++---
 .../custom/default_files/script.cmd           | 12 ++++++
 bci/web/vue/src/components/poc-editor.vue     | 41 +++++++++++--------
 .../{interaction_script.cmd => script.cmd}    |  2 +-
 .../Support/test}/interaction_script.cmd      |  4 +-
 5 files changed, 43 insertions(+), 26 deletions(-)
 create mode 100644 bci/evaluations/custom/default_files/script.cmd
 rename experiments/pages/Support/AutoGUI/{interaction_script.cmd => script.cmd} (94%)
 rename {bci/evaluations/custom/default_files => experiments/pages/Support/test}/interaction_script.cmd (79%)

diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index 085abf41..e4e9ff5c 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -57,7 +57,7 @@ def initialize_tests_and_interactions(dir_tree: dict) -> dict:
                 data = {}
 
                 if interaction_script := CustomEvaluationFramework.__get_interaction_script(project_path, experiment):
-                    data['interaction_script'] = interaction_script
+                    data['script'] = interaction_script
                 elif url_queue := CustomEvaluationFramework.__get_url_queue(project, project_path, experiment):
                     data['url_queue'] = url_queue
 
@@ -68,7 +68,7 @@ def initialize_tests_and_interactions(dir_tree: dict) -> dict:
 
     @staticmethod
     def __get_interaction_script(project_path: str, experiment: str) -> list[str] | None:
-        interaction_file_path = os.path.join(project_path, experiment, 'interaction_script.cmd')
+        interaction_file_path = os.path.join(project_path, experiment, 'script.cmd')
         if os.path.isfile(interaction_file_path):
             # If an interaction script is specified, it is parsed and used
             with open(interaction_file_path) as file:
@@ -97,7 +97,7 @@ def __get_url_queue(project: str, project_path: str, experiment: str) -> Optiona
     @staticmethod
     def is_runnable_experiment(project: str, poc: str, dir_tree: dict[str,dict], data: dict[str,str]) -> bool:
         # Always runnable if there is either an interaction script or url_queue present
-        if 'interaction_script' in data or 'url_queue' in data:
+        if 'script' in data or 'url_queue' in data:
             return True
 
         # Should have exactly one main folder otherwise
@@ -123,8 +123,8 @@ def perform_specific_evaluation(self, browser: Browser, params: TestParameters)
             experiment = self.tests_per_project[params.evaluation_configuration.project][params.mech_group]
 
             max_tries = 3
-            if 'interaction_script' in experiment:
-                interaction = Interaction(browser, experiment['interaction_script'], params)
+            if 'script' in experiment:
+                interaction = Interaction(browser, experiment['script'], params)
                 tries = 0
                 while tries < max_tries:
                     tries += 1
diff --git a/bci/evaluations/custom/default_files/script.cmd b/bci/evaluations/custom/default_files/script.cmd
new file mode 100644
index 00000000..749e7a21
--- /dev/null
+++ b/bci/evaluations/custom/default_files/script.cmd
@@ -0,0 +1,12 @@
+# TODO - add your interaction script using the commands
+
+# NAVIGATE url
+# CLICK_POSITION x y    where x and y are absolute numbers or screen percentages
+# CLICK element_id      where element_id is one of one, two, three, four, five, six
+# WRITE text
+# PRESS key
+# HOLD key
+# RELEASE key
+# HOTKEY key1 key2 ...
+# SLEEP seconds         where seconds is a float or an int
+# SCREENSHOT file_name
diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index a750fb01..167e0175 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -31,14 +31,24 @@
             // Example tree:
             // {
             //   'test.com': {
-            //     "path1": ["file1", "file2"],
-            //     "path2": ["file1"],
+            //     "path1": {
+            //        "file1": null,
+            //        "file2": null
+            //     },
+            //     "path2": {
+            //        "file1": null
+            //     },
             //   },
             //   'not.test': {
-            //     "path1": ["file1", "file2"],
-            //     "path2": ["file1"],
+            //     "path1": {
+            //        "file1": null,
+            //        "file2": null
+            //     },
+            //     "path2": {
+            //        "file1": null
+            //     },
             //   },
-            //  'interaction_script.cmd': 'interaction_script.cmd',
+            //  'script.cmd': null,
             // },
         },
         available_file_types: [
@@ -47,7 +57,7 @@
           'py',
         ],
         available_config_types: {
-          'interaction_script.cmd': 'Interaction script',
+          'script.cmd': 'Interaction script',
           'url_queue.txt': 'URL queue'
         },
         poc_tree_config: {
@@ -238,7 +248,7 @@
           console.error("Could not check config in undefined poc tree");
           return false;
         }
-        const arr = Object.keys(this.active_poc.tree).filter((domain) => ['url_queue.txt', 'interaction_script.cmd'].includes(domain));
+        const arr = Object.keys(this.active_poc.tree).filter((domain) => ['url_queue.txt', 'script.cmd'].includes(domain));
         return arr.length > 0;
       }
     },
@@ -277,17 +287,12 @@
       <ul class="relative flex flex-col text-gray-700 bg-white shadow-md w-96 rounded-md bg-clip-border dark:bg-dark-3 dark:text-white">
         <nav class="flex min-w-[240px] h-full flex-col gap-1 p-2 font-sans text-base font-normal text-blue-gray-700">
           <li v-for="([domain, pages]) in Object.entries(active_poc.tree).sort()">
-            <div v-if="domain === 'url_queue.txt' || domain === 'interaction_script.cmd'">
-              <div class="flex border-b-2 p-2 font-bold mb-2 hover:bg-gray-100 hover:bg-opacity-80 hover:text-blue-gray-900 hover:cursor-pointer focus:bg-blue-gray-50 focus:bg-opacity-80 focus:text-blue-gray-900" >
-                <div
-                    role="button"
-                    class="rounded-lg"
-                    @click="set_active_file(null, null, domain)"
-                  >
-                  <div class="w-full">
-                    {{ domain }}
-                  </div>
-                </div>
+            <div v-if="domain === 'url_queue.txt' || domain === 'script.cmd'">
+              <div
+                class="flex border-b-2 p-2 font-bold mb-2 hover:bg-gray-100 hover:bg-opacity-80 hover:text-blue-gray-900 hover:cursor-pointer focus:bg-blue-gray-50 focus:bg-opacity-80 focus:text-blue-gray-900"
+                role="button"
+                @click="set_active_file(null, null, domain)" >
+                {{ domain }}
               </div>
             </div>
             <ul v-else>
diff --git a/experiments/pages/Support/AutoGUI/interaction_script.cmd b/experiments/pages/Support/AutoGUI/script.cmd
similarity index 94%
rename from experiments/pages/Support/AutoGUI/interaction_script.cmd
rename to experiments/pages/Support/AutoGUI/script.cmd
index 91d6f21f..f72b0eff 100644
--- a/experiments/pages/Support/AutoGUI/interaction_script.cmd
+++ b/experiments/pages/Support/AutoGUI/script.cmd
@@ -15,4 +15,4 @@ HOLD v
 RELEASE v
 RELEASE ctrl
 
-PRESS Enter
\ No newline at end of file
+PRESS Enter
diff --git a/bci/evaluations/custom/default_files/interaction_script.cmd b/experiments/pages/Support/test/interaction_script.cmd
similarity index 79%
rename from bci/evaluations/custom/default_files/interaction_script.cmd
rename to experiments/pages/Support/test/interaction_script.cmd
index 63ad6d9b..749e7a21 100644
--- a/bci/evaluations/custom/default_files/interaction_script.cmd
+++ b/experiments/pages/Support/test/interaction_script.cmd
@@ -1,4 +1,4 @@
-# TODO - add your interaction script using the commands 
+# TODO - add your interaction script using the commands
 
 # NAVIGATE url
 # CLICK_POSITION x y    where x and y are absolute numbers or screen percentages
@@ -9,4 +9,4 @@
 # RELEASE key
 # HOTKEY key1 key2 ...
 # SLEEP seconds         where seconds is a float or an int
-# SCREENSHOT file_name
\ No newline at end of file
+# SCREENSHOT file_name

From 69c758c0cf543140250a098027b265f3c30014d0 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Wed, 13 Nov 2024 12:22:09 +0000
Subject: [PATCH 39/57] Remove test experiment

---
 .../pages/Support/test/interaction_script.cmd        | 12 ------------
 1 file changed, 12 deletions(-)
 delete mode 100644 experiments/pages/Support/test/interaction_script.cmd

diff --git a/experiments/pages/Support/test/interaction_script.cmd b/experiments/pages/Support/test/interaction_script.cmd
deleted file mode 100644
index 749e7a21..00000000
--- a/experiments/pages/Support/test/interaction_script.cmd
+++ /dev/null
@@ -1,12 +0,0 @@
-# TODO - add your interaction script using the commands
-
-# NAVIGATE url
-# CLICK_POSITION x y    where x and y are absolute numbers or screen percentages
-# CLICK element_id      where element_id is one of one, two, three, four, five, six
-# WRITE text
-# PRESS key
-# HOLD key
-# RELEASE key
-# HOTKEY key1 key2 ...
-# SLEEP seconds         where seconds is a float or an int
-# SCREENSHOT file_name

From 2a34025fd3e1440c5e7884ee2f537ecb5d8a503d Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Wed, 13 Nov 2024 15:20:12 +0000
Subject: [PATCH 40/57] Add button to create a new project

---
 bci/evaluations/custom/custom_evaluation.py   | 14 +++++
 bci/main.py                                   |  6 +-
 bci/web/blueprints/api.py                     | 19 ++++++
 bci/web/clients.py                            |  8 ++-
 bci/web/vue/src/App.vue                       | 62 ++++++++++++++++---
 bci/web/vue/src/components/section-header.vue |  2 +-
 6 files changed, 100 insertions(+), 11 deletions(-)

diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index e4e9ff5c..da9cd812 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -166,6 +166,20 @@ def get_mech_groups(self, project: str) -> list[tuple[str, bool]]:
     def get_projects(self) -> list[str]:
         return sorted(list(self.tests_per_project.keys()))
 
+    def create_empty_project(self, project_name: str) -> bool:
+        if project_name is None or project_name == '':
+            logger.error('Given project name is invalid')
+            return False
+
+        if project_name in self.dir_tree:
+            logger.error(f"Given project name '{project_name}' already exists")
+            return False
+
+        new_project_path = os.path.join(Global.custom_page_folder, project_name)
+        os.mkdir(new_project_path)
+        self.sync_with_folders()
+        return True
+
     def get_poc_structure(self, project: str, poc: str) -> dict:
         return self.dir_tree[project][poc]
 
diff --git a/bci/main.py b/bci/main.py
index fddb53ae..915037b9 100644
--- a/bci/main.py
+++ b/bci/main.py
@@ -91,6 +91,10 @@ def get_mech_groups_of_evaluation_framework(evaluation_name: str, project) -> li
     def get_projects_of_custom_framework() -> list[str]:
         return Main.master.evaluation_framework.get_projects()
 
+    @staticmethod
+    def create_empty_project(project_name: str) -> bool:
+        return Main.master.evaluation_framework.create_empty_project(project_name)
+
     @staticmethod
     def convert_to_plotparams(data: dict) -> PlotParameters:
         if data.get("lower_version", None) and data.get("upper_version", None):
@@ -155,7 +159,7 @@ def get_available_domains() -> list[str]:
     @staticmethod
     def add_page(project: str, poc: str, domain: str, path: str, file_type: str) -> bool:
         return Main.master.evaluation_framework.add_page(project, poc, domain, path, file_type)
-    
+
     @staticmethod
     def add_config(project: str, poc: str, type: str) -> bool:
         return Main.master.evaluation_framework.add_config(project, poc, type)
diff --git a/bci/web/blueprints/api.py b/bci/web/blueprints/api.py
index accc66d4..0b901d4a 100644
--- a/bci/web/blueprints/api.py
+++ b/bci/web/blueprints/api.py
@@ -135,6 +135,20 @@ def get_projects():
     }
 
 
+@api.route('/projects/', methods=['POST'])
+def create_project():
+    if request.json is None:
+        return {
+            'status': 'NOK',
+            'msg': "No parameters found"
+        }
+    project_name = request.json.get('project_name')
+    return {
+        'status': 'OK',
+        'projects': bci_api.create_empty_project(project_name)
+    }
+
+
 @api.route('/system/', methods=['GET'])
 def get_system_info():
     return {
@@ -240,6 +254,11 @@ def add_page(project: str, poc: str):
 
 @api.route('/poc/<string:project>/<string:poc>/config', methods=['POST'])
 def add_config(project: str, poc: str):
+    if request.json is None:
+        return {
+            'status': 'NOK',
+            'msg': "No parameters found"
+        }
     data = request.json.copy()
     success = bci_api.add_config(project, poc, data['type'])
     if success:
diff --git a/bci/web/clients.py b/bci/web/clients.py
index eee5d240..9dad0fd8 100644
--- a/bci/web/clients.py
+++ b/bci/web/clients.py
@@ -1,5 +1,6 @@
 import json
 import threading
+from venv import logger
 
 from simple_websocket import Server
 
@@ -86,7 +87,12 @@ def push_info_to_all(*requested_vars: str):
     def push_experiments(ws_client: Server):
         from bci.main import Main as bci_api
 
-        project = Clients.__clients[ws_client].get('project', None)
+        client_info = Clients.__clients[ws_client]
+        if client_info is None:
+            logger.error('Could not find any associated info for this client')
+            return
+
+        project = client_info.get('project', None)
         if project:
             experiments = bci_api.get_mech_groups_of_evaluation_framework('custom', project)
             ws_client.send(json.dumps({'update': {'experiments': experiments}}))
diff --git a/bci/web/vue/src/App.vue b/bci/web/vue/src/App.vue
index cac94259..a7369d1b 100644
--- a/bci/web/vue/src/App.vue
+++ b/bci/web/vue/src/App.vue
@@ -78,7 +78,8 @@ export default {
         project: null,
       },
       dialog: {
-        new_experiment_name: null
+        new_experiment_name: null,
+        new_project_name: null
       },
       darkmode: null,
       darkmode_toggle: null,
@@ -131,9 +132,6 @@ export default {
     },
   },
   watch: {
-    "selected.project": function (val) {
-      this.set_curr_project(val);
-    },
     "selected.experiment": function (val) {
       if (val !== null) {
         this.hide_poc_editor = false;
@@ -235,7 +233,10 @@ export default {
           "get": ["all"],
         });
         // This might be a re-open after connection loss, which means we might have to propagate our params again
-        this.propagate_new_params()
+        if (this.selected.project !== null) {
+          this.set_curr_project(this.selected.project);
+        }
+        this.propagate_new_params();
       });
       websocket.addEventListener("message", () => {
         const data = JSON.parse(event.data);
@@ -288,12 +289,15 @@ export default {
         localStorage.setItem('theme', 'light');
       }
     },
-    get_projects() {
+    get_projects(cb) {
       const path = `/api/projects/`;
       axios.get(path)
         .then((res) => {
           if (res.data.status == "OK") {
             this.projects = res.data.projects;
+            if (cb !== undefined) {
+              cb();
+            }
           }
         })
         .catch((error) => {
@@ -336,11 +340,20 @@ export default {
         console.log("Missing plot parameters: ", this.missing_plot_params);
       }
     },
+    project_dropdown_change(event) {
+      const option = event.target.value;
+      if (option == "Create new project...") {
+        create_project_dialog.showModal();
+      } else {
+        this.set_curr_project(option)
+      }
+    },
     set_curr_project(project) {
       this.eval_params.project = project;
       this.send_with_socket({
         "select_project": project
       })
+      this.selected.project = project;
       this.eval_params.tests = [];
     },
     set_curr_browser(browser) {
@@ -389,7 +402,21 @@ export default {
         this.dialog.new_experiment_name = null;
       })
       .catch((error) => {
-        console.log('Could not create new experiment');
+        console.error('Could not create new experiment');
+      });
+    },
+    create_new_project() {
+      const url = `/api/projects/`;
+      const new_project_name = this.dialog.new_project_name;
+      axios.post(url, {'project_name': new_project_name})
+      .then((res) => {
+        this.dialog.new_project_name = null;
+        this.get_projects(() => {
+          this.set_curr_project(new_project_name);
+        });
+      })
+      .catch((error) => {
+        console.error('Could not create new project', error);
       });
     },
   },
@@ -465,9 +492,10 @@ export default {
       <div class="form-section flex flex-col grow h-0">
         <section-header section="experiments" class="w-1/2"></section-header>
 
-        <select class="mb-2" v-model="selected.project">
+        <select id="project_dropdown" class="mb-2" @change="project_dropdown_change" v-model="selected.project">
           <option disabled value="">Select a project</option>
           <option v-for="project in projects">{{ project }}</option>
+          <option>Create new project...</option>
         </select>
 
         <div class="h-0 grow overflow-y-auto overflow-x-hidden">
@@ -683,5 +711,23 @@ export default {
       </div>
     </form>
   </dialog>
+
+  <!-- Create project dialog -->
+  <dialog id="create_project_dialog" class="dialog">
+    <form method="dialog" @submit="create_new_project">
+      <p>
+        <label>
+          <div class="pb-5">
+            Enter new project name:
+          </div>
+          <input type="text" v-model="dialog.new_project_name" class="input-box" required autocomplete="off" />
+        </label>
+      </p>
+      <div class="flex pt-3">
+        <input type="submit" value="Create project" class="button m-2 w-full">
+        <input type="button" value="Cancel" class="button m-2" onclick="create_project_dialog.close()">
+      </div>
+    </form>
+  </dialog>
 </template>
 
diff --git a/bci/web/vue/src/components/section-header.vue b/bci/web/vue/src/components/section-header.vue
index 916479aa..0cd95c7d 100644
--- a/bci/web/vue/src/components/section-header.vue
+++ b/bci/web/vue/src/components/section-header.vue
@@ -30,7 +30,7 @@
           },
           "experiments": {
             "title": "Experiments",
-            "tooltip": "Pick a project from the dropdown menu to access all available experiments. Then, mark the experiments you wish to conduct. Keep in mind that if multiple experiments are chosen, only a binary sequence will be performed. For a binary search or composite search, select only one experiment."
+            "tooltip": "Pick a project from the dropdown menu to access all available experiments. Then, mark the experiments you wish to conduct. A selection of multiple experiments will be conducted one by one."
           },
           "parallel_containers": {
             "title": "Number of parallel containers",

From f6e34ccf33f79850d6f32ba2ed3529cfe7affc0f Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Wed, 13 Nov 2024 15:33:26 +0000
Subject: [PATCH 41/57] Automatically create empty collection when trying to
 retrieve non-existing collection

---
 bci/database/mongo/mongodb.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bci/database/mongo/mongodb.py b/bci/database/mongo/mongodb.py
index 6b875831..08e3d2d5 100644
--- a/bci/database/mongo/mongodb.py
+++ b/bci/database/mongo/mongodb.py
@@ -178,7 +178,7 @@ def has_result(self, params: TestParameters) -> bool:
     def get_evaluated_states(
         self, params: EvaluationParameters, boundary_states: tuple[State, State], outcome_checker: OutcomeChecker
     ) -> list[State]:
-        collection = self.get_collection(params.database_collection)
+        collection = self.get_collection(params.database_collection, create_if_not_found=True)
         query = {
             'browser_config': params.browser_configuration.browser_setting,
             'mech_group': params.evaluation_range.mech_group,
@@ -308,7 +308,7 @@ def get_build_id_firefox(self, state: State):
         return result['build_id']
 
     def get_documents_for_plotting(self, params: PlotParameters, releases: bool = False):
-        collection = self.get_collection(params.database_collection)
+        collection = self.get_collection(params.database_collection, create_if_not_found=True)
         query = {
             'mech_group': params.mech_group,
             'browser_config': params.browser_config,

From 301da7e1b35c845c1d67524d36608c3d4aa7d8cc Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Wed, 13 Nov 2024 18:02:37 +0000
Subject: [PATCH 42/57] Fix issue where conditional /report/if endpoints
 couldn't be reached

---
 bci/evaluations/collectors/requests.py | 4 +++-
 bci/web/blueprints/experiments.py      | 6 +++---
 nginx/config/experiments.conf          | 2 +-
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/bci/evaluations/collectors/requests.py b/bci/evaluations/collectors/requests.py
index 1e6906ba..db998037 100644
--- a/bci/evaluations/collectors/requests.py
+++ b/bci/evaluations/collectors/requests.py
@@ -73,7 +73,9 @@ def start(self):
 
     def stop(self):
         data = []
-        regex = r'bughog_(.+)=(.+)'
+        # Important: we only consider requests to the /report/ endpoint where the bughog parameter immediately follows.
+        # Otherwise conditional endpoints (e.g., /report/if/Referer/) cause false positives.
+        regex = r'/report/\?bughog_(.+)=(.+)'
         if self.__httpd:
             self.__httpd.shutdown()
             if self.__thread:
diff --git a/bci/web/blueprints/experiments.py b/bci/web/blueprints/experiments.py
index b5cb5945..a5942403 100644
--- a/bci/web/blueprints/experiments.py
+++ b/bci/web/blueprints/experiments.py
@@ -91,7 +91,7 @@ def report_leak_if_using_http(target_scheme):
     used_scheme = request.headers.get("X-Forwarded-Proto")
     params = __get_all_GET_parameters(request)
     if used_scheme == target_scheme:
-        return "Redirect", 307, {"Location": url_for("experiments.report", **params)}
+        return "Redirect", 307, {"Location": url_for("experiments.report_endpoint", **params)}
     else:
         return f"Request was received over {used_scheme}, instead of {target_scheme}", 200, {}
 
@@ -109,7 +109,7 @@ def report_leak_if_present(expected_header_name: str):
         "Redirect",
         307,
         {
-            "Location": url_for("experiments.report", **params),
+            "Location": url_for("experiments.report_endpoint", **params),
             "Allow-CSP-From": "*",
         },
     )
@@ -134,7 +134,7 @@ def report_leak_if_contains(expected_header_name: str, expected_header_value: st
         "Redirect",
         307,
         {
-            "Location": url_for("experiments.report", **params),
+            "Location": url_for("experiments.report_endpoint", **params),
             "Allow-CSP-From": "*",
         },
     )
diff --git a/nginx/config/experiments.conf b/nginx/config/experiments.conf
index 01c40960..01c45c6b 100644
--- a/nginx/config/experiments.conf
+++ b/nginx/config/experiments.conf
@@ -19,7 +19,7 @@ location @resources {
 }
 
 # Reporting endpoint
-location ~ /report/?[^/]*$ {
+location ~ /report/.*$ {
     proxy_pass http://core:5000;
     proxy_set_header Host $host;
     proxy_set_header X-Real-IP $remote_addr;

From cf43c7d5d791b582f54ac5287a866b456b67f127 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Fri, 15 Nov 2024 12:53:55 +0000
Subject: [PATCH 43/57] Fix creation of python server file

---
 bci/evaluations/custom/custom_evaluation.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index da9cd812..55df01c8 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -221,11 +221,17 @@ def add_page(self, project: str, poc: str, domain: str, path: str, file_type: st
         domain_path = os.path.join(Global.custom_page_folder, project, poc, domain)
         if not os.path.exists(domain_path):
             os.makedirs(domain_path)
-        page_path = os.path.join(domain_path, path)
-        if not os.path.exists(page_path):
-            os.makedirs(page_path)
-        new_file_name = f'index.{file_type}'
-        file_path = os.path.join(page_path, new_file_name)
+
+        if file_type == 'py':
+            file_name = path if path.endswith('.py') else path + '.py'
+            file_path = os.path.join(domain_path, file_name)
+        else:
+            page_path = os.path.join(domain_path, path)
+            if not os.path.exists(page_path):
+                os.makedirs(page_path)
+            new_file_name = f'index.{file_type}'
+            file_path = os.path.join(page_path, new_file_name)
+
         if os.path.exists(file_path):
             return False
         with open(file_path, 'w') as file:

From 6c275f470b23849b62e9e7246dfe15629719d0b2 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Fri, 15 Nov 2024 13:26:47 +0000
Subject: [PATCH 44/57] Clear editor when changing poc or project

---
 bci/web/vue/src/components/poc-editor.vue | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 167e0175..ecdd6e44 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -268,6 +268,18 @@
       "poc": function(val) {
         this.editor.setValue();
         this.editor.clearSelection();
+        this.active_file.name = null;
+        this.active_file.content = null;
+        this.update_poc_tree(val);
+      },
+      "project": function(val) {
+        this.editor.setValue();
+        this.editor.clearSelection();
+        this.active_file.name = null;
+        this.active_file.content = null;
+        this.active_poc.name = null;
+        this.active_poc.active_domain: null;
+        this.active_poc.active_path: null;
         this.update_poc_tree(val);
       },
     },

From 849a6f282d1e6df61b8aeb577300019f6d365d45 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Fri, 15 Nov 2024 16:15:31 +0000
Subject: [PATCH 45/57] Fix two typos

---
 bci/web/vue/src/components/poc-editor.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index ecdd6e44..369afc74 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -278,8 +278,8 @@
         this.active_file.name = null;
         this.active_file.content = null;
         this.active_poc.name = null;
-        this.active_poc.active_domain: null;
-        this.active_poc.active_path: null;
+        this.active_poc.active_domain = null;
+        this.active_poc.active_path = null;
         this.update_poc_tree(val);
       },
     },

From 968dfc384e7b514fca281ee3fb61fc3763c40108 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Fri, 22 Nov 2024 21:26:26 +0000
Subject: [PATCH 46/57] Enable various advanced options for release version
 evaluation

---
 bci/web/vue/src/App.vue                   | 8 ++++----
 bci/web/vue/src/components/poc-editor.vue | 6 ++++++
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/bci/web/vue/src/App.vue b/bci/web/vue/src/App.vue
index a7369d1b..b2b56a18 100644
--- a/bci/web/vue/src/App.vue
+++ b/bci/web/vue/src/App.vue
@@ -633,21 +633,21 @@ export default {
 
               <div class="radio-item">
                 <input v-model="eval_params.search_strategy" type="radio" id="bin_seq" name="search_strategy_option"
-                  value="bgb_sequence" :disabled="this.eval_params.only_release_revisions">
+                  value="bgb_sequence">
                 <label for="bgb_sequence">BGB sequence</label>
                 <tooltip tooltip="bgb_sequence"></tooltip>
               </div>
 
               <div class="radio-item">
                 <input v-model="eval_params.search_strategy" type="radio" id="bgb_search" name="search_strategy_option"
-                  value="bgb_search" :disabled="this.eval_params.only_release_revisions">
+                  value="bgb_search">
                 <label for="bgb_search">BGB search</label>
                 <tooltip tooltip="bgb_search"></tooltip>
               </div>
 
               <div class="radio-item">
                 <input v-model="eval_params.search_strategy" type="radio" id="comp_search" name="search_strategy_option"
-                  value="comp_search" :disabled="this.eval_params.only_release_revisions">
+                  value="comp_search">
                 <label for="comp_search">Composite search</label>
                 <tooltip tooltip="comp_search"></tooltip>
               </div>
@@ -657,7 +657,7 @@ export default {
                 <label for="sequence_limit" class="mb-0 align-middle">Sequence limit</label>
                 <tooltip tooltip="sequence_limit"></tooltip>
               </div>
-              <input v-model.number="eval_params.sequence_limit" class="input-box" type="number" min="1" max="10000" :disabled="this.eval_params.only_release_revisions">
+              <input v-model.number="eval_params.sequence_limit" class="input-box" type="number" min="1" max="10000">
             </div>
 
             <div class="form-subsection">
diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 369afc74..14bb2ef7 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -265,6 +265,12 @@
           this.editor.setTheme("ace/theme/xcode");
         }
       },
+      "active_file.name": function (val) {
+        // Make editor readOnly when no file is selected
+        this.editor.setOptions({
+          "readOnly": val === null
+        });
+      },
       "poc": function(val) {
         this.editor.setValue();
         this.editor.clearSelection();

From 1e24fb04923ad80da42bd9cb53b52de722f6aea5 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Fri, 22 Nov 2024 22:38:24 +0000
Subject: [PATCH 47/57] Abandon hacky nginx request splitting in favor of the
 `mirror` directive and add favicon for experiment pages

---
 bci/web/vue/public/.gitkeep                   |   0
 .../vue/public => experiments/res}/bughog.ico | Bin
 nginx/config/core_dev.conf                    |   4 ++++
 nginx/config/core_prod.conf                   |   4 ++++
 nginx/config/experiments.conf                 |  21 +++++++++---------
 nginx/config/notify_collector.conf            |   9 ++------
 6 files changed, 21 insertions(+), 17 deletions(-)
 create mode 100644 bci/web/vue/public/.gitkeep
 rename {bci/web/vue/public => experiments/res}/bughog.ico (100%)

diff --git a/bci/web/vue/public/.gitkeep b/bci/web/vue/public/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/bci/web/vue/public/bughog.ico b/experiments/res/bughog.ico
similarity index 100%
rename from bci/web/vue/public/bughog.ico
rename to experiments/res/bughog.ico
diff --git a/nginx/config/core_dev.conf b/nginx/config/core_dev.conf
index 3e1da787..78a0ca80 100644
--- a/nginx/config/core_dev.conf
+++ b/nginx/config/core_dev.conf
@@ -1,5 +1,9 @@
 access_log /logs/nginx-access-api.log default_format;
 
+location = /favicon.ico {
+    alias /www/data/res/bughog.ico;
+}
+
 location / {
     proxy_pass http://node:5173;
     proxy_set_header Host $host;
diff --git a/nginx/config/core_prod.conf b/nginx/config/core_prod.conf
index 835f344d..43ce77b9 100644
--- a/nginx/config/core_prod.conf
+++ b/nginx/config/core_prod.conf
@@ -1,5 +1,9 @@
 access_log /logs/nginx-access-api.log default_format;
 
+location = /favicon.ico {
+    alias /www/data/res/bughog.ico;
+}
+
 location / {
     root /www/data;
 }
diff --git a/nginx/config/experiments.conf b/nginx/config/experiments.conf
index 01c45c6b..36531f6c 100644
--- a/nginx/config/experiments.conf
+++ b/nginx/config/experiments.conf
@@ -1,5 +1,9 @@
 access_log /logs/nginx-access-poc.log default_format;
 
+location = /favicon.ico {
+    alias /www/data/res/bughog.ico;
+}
+
 # Home
 location = / {
     proxy_pass http://core:5000;
@@ -10,12 +14,8 @@ location = / {
 
 # Shared static resources
 location ^~ /res/ {
-    include /etc/nginx/config/notify_collector.conf;
-    error_page 504 =200 @resources;
-}
-
-location @resources {
     root /www/data;
+    mirror /notify_collector;
 }
 
 # Reporting endpoint
@@ -42,11 +42,6 @@ location ~ index\.(html|js)$ {
 }
 
 location ~ ^/[^/]+/[^/]+/[^/]+/?$ {
-    include /etc/nginx/config/notify_collector.conf;
-    error_page 504 @experiment;
-}
-
-location @experiment {
     root /www/data/pages;
     index index.html index.js;
     # Rewrite URLs conform to experiment file structure
@@ -75,4 +70,10 @@ location @experiment {
             ngx.log(ngx.WARN, "Could not find headers: " .. file_path)
         end
     }
+
+    mirror /notify_collector;
+}
+
+location = /notify_collector {
+    include /etc/nginx/config/notify_collector.conf;
 }
diff --git a/nginx/config/notify_collector.conf b/nginx/config/notify_collector.conf
index 78bd8fc0..540ba0ba 100644
--- a/nginx/config/notify_collector.conf
+++ b/nginx/config/notify_collector.conf
@@ -1,8 +1,5 @@
 # We want to notify worker-specific request collectors of every request to our experiment server.
-# Hacky solution: pretend that the collector is not reachable and use fallback to serve experiment page.
-# So:
-# 1. NGINX will send request to request collector of worker.
-# 2. NGINX will serve the experiment page.
+# This module is called for every received experiment-related request by using `mirror`.
 
 proxy_pass http://$remote_addr:5001/report/;
 proxy_set_header X-Real-IP $remote_addr;
@@ -23,8 +20,6 @@ set $content '"content": "${request_body_data}"';
 set $report '{${url}, ${method}, ${content}}';
 proxy_set_body $report;
 
-# We don't need any response, we merely want to notify
 proxy_connect_timeout 2s;
 proxy_send_timeout 2s;
-proxy_read_timeout 0s;  # Force a 504 by setting timeout to 0
-
+proxy_read_timeout 2s;

From 1272591b168ac5feed38500d55fb360ad198abed Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Mon, 25 Nov 2024 14:40:21 +0000
Subject: [PATCH 48/57] Remove pseudo-interface for master.py + small fixes +
 cleanup

---
 bci/analysis/plot_factory.py              |   8 +-
 bci/app.py                                |  17 +-
 bci/configuration.py                      |  13 +-
 bci/database/mongo/mongodb.py             |   1 -
 bci/evaluations/logic.py                  |  29 ++
 bci/main.py                               | 337 ++++++++++++----------
 bci/master.py                             | 169 -----------
 bci/web/blueprints/api.py                 |  80 +++--
 bci/web/clients.py                        |  39 +--
 bci/web/vue/src/App.vue                   |   3 +-
 bci/web/vue/src/components/poc-editor.vue |   1 -
 11 files changed, 306 insertions(+), 391 deletions(-)
 delete mode 100644 bci/master.py

diff --git a/bci/analysis/plot_factory.py b/bci/analysis/plot_factory.py
index 84a0f045..7fa51739 100644
--- a/bci/analysis/plot_factory.py
+++ b/bci/analysis/plot_factory.py
@@ -5,14 +5,14 @@
 class PlotFactory:
 
     @staticmethod
-    def get_plot_revision_data(params: PlotParameters, db: MongoDB) -> dict:
-        revision_docs = db.get_documents_for_plotting(params)
+    def get_plot_revision_data(params: PlotParameters) -> dict:
+        revision_docs = MongoDB().get_documents_for_plotting(params)
         revision_results = PlotFactory.__add_outcome_info(params, revision_docs)
         return revision_results
 
     @staticmethod
-    def get_plot_version_data(params: PlotParameters, db: MongoDB) -> dict:
-        version_docs = db.get_documents_for_plotting(params, releases=True)
+    def get_plot_version_data(params: PlotParameters) -> dict:
+        version_docs = MongoDB().get_documents_for_plotting(params, releases=True)
         version_results = PlotFactory.__add_outcome_info(params, version_docs)
         return version_results
 
diff --git a/bci/app.py b/bci/app.py
index 9e504cbe..5f037be5 100644
--- a/bci/app.py
+++ b/bci/app.py
@@ -3,12 +3,20 @@
 from flask import Flask
 from flask_sock import Sock
 
-from bci.main import Main as bci_api
+from bci.configuration import Global, Loggers
+from bci.main import Main
 
 sock = Sock()
 
+
 def create_app():
-    bci_api.initialize()
+    Loggers.configure_loggers()
+
+    if not Global.check_required_env_parameters():
+        raise Exception('Not all required environment variables are available')
+
+    # Instantiate main object and add to global flask context
+    main = Main()
 
     # Blueprint modules are only imported after loggers are configured
     from bci.web.blueprints.api import api
@@ -16,6 +24,7 @@ def create_app():
 
     app = Flask(__name__)
     # We don't store anything sensitive in the session, so we can use a simple secret key
+    app.config['main'] = main
     app.secret_key = 'secret_key'
 
     app.register_blueprint(api)
@@ -23,8 +32,8 @@ def create_app():
     sock.init_app(app)
 
     # Configure signal handlers
-    signal.signal(signal.SIGTERM, bci_api.sigint_handler)
-    signal.signal(signal.SIGINT, bci_api.sigint_handler)
+    signal.signal(signal.SIGTERM, main.sigint_handler)
+    signal.signal(signal.SIGINT, main.sigint_handler)
 
     return app
 
diff --git a/bci/configuration.py b/bci/configuration.py
index c8472c04..166e0e03 100644
--- a/bci/configuration.py
+++ b/bci/configuration.py
@@ -170,5 +170,14 @@ def handle_exception(exc_type, exc_value, exc_traceback):
         bci_logger.debug('Loggers initialized')
 
     @staticmethod
-    def get_formatted_buffer_logs() -> list[str]:
-        return [Loggers.formatter.format(record) for record in Loggers.memory_handler.buffer]
+    def get_logs() -> list[str]:
+        return list(
+            map(
+                lambda x: Loggers.format_to_user_log(x.__dict__),
+                Loggers.memory_handler.buffer,
+            )
+        )
+
+    @staticmethod
+    def format_to_user_log(log: dict) -> str:
+        return f'[{log["asctime"]}] [{log["levelname"]}] {log["name"]}: {log["msg"]}'
diff --git a/bci/database/mongo/mongodb.py b/bci/database/mongo/mongodb.py
index 08e3d2d5..6351e79c 100644
--- a/bci/database/mongo/mongodb.py
+++ b/bci/database/mongo/mongodb.py
@@ -18,7 +18,6 @@
     StateResult,
     TestParameters,
     TestResult,
-    WorkerParameters,
 )
 from bci.evaluations.outcome_checker import OutcomeChecker
 from bci.version_control.states.state import State, StateCondition
diff --git a/bci/evaluations/logic.py b/bci/evaluations/logic.py
index ad6f0e87..8c1cbe36 100644
--- a/bci/evaluations/logic.py
+++ b/bci/evaluations/logic.py
@@ -228,6 +228,35 @@ class PlotParameters:
     dirty_allowed: bool = True
     target_cookie_name: Optional[str] = None
 
+    @staticmethod
+    def from_dict(data: dict) -> PlotParameters:
+        if data.get("lower_version", None) and data.get("upper_version", None):
+            major_version_range = (data["lower_version"], data["upper_version"])
+        else:
+            major_version_range = None
+        if data.get("lower_revision_nb", None) and data.get("upper_revision_nb", None):
+            revision_number_range = (
+                data["lower_revision_nb"],
+                data["upper_revision_nb"],
+            )
+        else:
+            revision_number_range = None
+        return PlotParameters(
+            data.get("plot_mech_group"),
+            data.get("target_mech_id"),
+            data.get("browser_name"),
+            data.get("db_collection"),
+            major_version_range=major_version_range,
+            revision_number_range=revision_number_range,
+            browser_config=data.get("browser_setting", "default"),
+            extensions=data.get("extensions", []),
+            cli_options=data.get("cli_options", []),
+            dirty_allowed=data.get("dirty_allowed", True),
+            target_cookie_name=None
+            if data.get("check_for") == "request"
+            else data.get("target_cookie_name", "generic"),
+        )
+
 
 @staticmethod
 def evaluation_factory(kwargs: ImmutableMultiDict) -> list[EvaluationParameters]:
diff --git a/bci/main.py b/bci/main.py
index 915037b9..0c27412e 100644
--- a/bci/main.py
+++ b/bci/main.py
@@ -1,169 +1,188 @@
 import logging
 
-import bci.browser.binary.factory as binary_factory
-from bci.analysis.plot_factory import PlotFactory
-from bci.browser.support import get_chromium_support, get_firefox_support
+import bci.database.mongo.container as mongodb_container
 from bci.configuration import Global, Loggers
-from bci.database.mongo.mongodb import MongoDB
-from bci.evaluations.logic import EvaluationParameters, PlotParameters
-from bci.master import Master
+from bci.database.mongo.mongodb import MongoDB, ServerException
+from bci.database.mongo.revision_cache import RevisionCache
+from bci.distribution.worker_manager import WorkerManager
+from bci.evaluations.custom.custom_evaluation import CustomEvaluationFramework
+from bci.evaluations.logic import (
+    DatabaseParameters,
+    EvaluationParameters,
+)
+from bci.evaluations.outcome_checker import OutcomeChecker
+from bci.search_strategy.bgb_search import BiggestGapBisectionSearch
+from bci.search_strategy.bgb_sequence import BiggestGapBisectionSequence
+from bci.search_strategy.composite_search import CompositeSearch
+from bci.search_strategy.sequence_strategy import SequenceFinished, SequenceStrategy
+from bci.version_control.factory import StateFactory
+from bci.version_control.states.revisions.firefox import BINARY_AVAILABILITY_MAPPING
+from bci.web.clients import Clients
 
 logger = logging.getLogger(__name__)
 
 
 class Main:
-    loggers = None
-    master = None
-
-    @staticmethod
-    def initialize():
-        Main.loggers = Loggers()
-        Main.loggers.configure_loggers()
-        if Global.check_required_env_parameters():
-            Main.master = Master()
-
-    @staticmethod
-    def is_ready() -> bool:
-        return Main.master is not None
-
-    @staticmethod
-    def run(params: EvaluationParameters):
-        Main.master.run(params)
-
-    @staticmethod
-    def stop_gracefully():
-        Main.master.activate_stop_gracefully()
-
-    @staticmethod
-    def stop_forcefully():
-        Main.master.activate_stop_forcefully()
-
-    @staticmethod
-    def get_state() -> str:
-        return Main.master.state
-
-    @staticmethod
-    def connect_to_database():
-        return Main.master.connect_to_database()
-
-    @staticmethod
-    def get_logs() -> list[str]:
-        return list(
-            map(
-                lambda x: Main.format_to_user_log(x.__dict__),
-                Loggers.memory_handler.buffer,
-            )
-        )
-
-    @staticmethod
-    def format_to_user_log(log: dict) -> str:
-        return f'[{log["asctime"]}] [{log["levelname"]}] {log["name"]}: {log["msg"]}'
-
-    @staticmethod
-    def get_database_info() -> dict:
-        return MongoDB().get_info()
-
-    @staticmethod
-    def get_browser_support() -> list[dict]:
-        return [get_chromium_support(), get_firefox_support()]
-
-    @staticmethod
-    def list_downloaded_binaries(browser):
-        return binary_factory.list_downloaded_binaries(browser)
-
-    @staticmethod
-    def list_artisanal_binaries(browser):
-        return binary_factory.list_artisanal_binaries(browser)
-
-    @staticmethod
-    def update_artisanal_binaries(browser):
-        return binary_factory.update_artisanal_binaries(browser)
-
-    @staticmethod
-    def download_online_binary(browser, rev_number):
-        binary_factory.download_online_binary(browser, rev_number)
-
-    @staticmethod
-    def get_mech_groups_of_evaluation_framework(evaluation_name: str, project) -> list[tuple[str, bool]]:
-        return Main.master.evaluation_framework.get_mech_groups(project)
-
-    @staticmethod
-    def get_projects_of_custom_framework() -> list[str]:
-        return Main.master.evaluation_framework.get_projects()
-
-    @staticmethod
-    def create_empty_project(project_name: str) -> bool:
-        return Main.master.evaluation_framework.create_empty_project(project_name)
-
-    @staticmethod
-    def convert_to_plotparams(data: dict) -> PlotParameters:
-        if data.get("lower_version", None) and data.get("upper_version", None):
-            major_version_range = (data["lower_version"], data["upper_version"])
+    def __init__(self) -> None:
+        self.state = {'is_running': False, 'reason': 'init', 'status': 'idle'}
+
+        self.stop_gracefully = False
+        self.stop_forcefully = False
+
+        self.firefox_build = None
+        self.chromium_build = None
+
+        self.eval_queue = []
+
+        Global.initialize_folders()
+        self.db_connection_params = Global.get_database_params()
+        self.connect_to_database(self.db_connection_params)
+        RevisionCache.store_firefox_binary_availability(BINARY_AVAILABILITY_MAPPING)  # TODO: find better place
+        self.evaluation_framework = CustomEvaluationFramework()
+        logger.info('BugHog is ready!')
+
+    def connect_to_database(self, db_connection_params: DatabaseParameters) -> None:
+        try:
+            MongoDB().connect(db_connection_params)
+        except ServerException:
+            logger.error('Could not connect to database.', exc_info=True)
+
+    def run(self, eval_params_list: list[EvaluationParameters]) -> None:
+        # Sequence_configuration settings are the same over evaluation parameters (quick fix)
+        worker_manager = WorkerManager(eval_params_list[0].sequence_configuration.nb_of_containers)
+        self.stop_gracefully = False
+        self.stop_forcefully = False
+        try:
+            self.__init_eval_queue(eval_params_list)
+            for eval_params in eval_params_list:
+                if self.stop_gracefully or self.stop_forcefully:
+                    break
+                self.__update_eval_queue(eval_params.evaluation_range.mech_group, 'active')
+                self.__update_state(is_running=True, reason='user', status='running', queue=self.eval_queue)
+                self.run_single_evaluation(eval_params, worker_manager)
+
+        except Exception as e:
+            logger.critical('A critical error occurred', exc_info=True)
+            raise e
+        finally:
+            # Gracefully exit
+            if self.stop_gracefully:
+                logger.info('Gracefully stopping experiment queue due to user end signal...')
+                self.state['reason'] = 'user'
+            if self.stop_forcefully:
+                logger.info('Forcefully stopping experiment queue due to user end signal...')
+                self.state['reason'] = 'user'
+                worker_manager.forcefully_stop_all_running_containers()
+            else:
+                logger.info('Gracefully stopping experiment queue since last experiment started.')
+            # MongoDB.disconnect()
+            logger.info('Waiting for remaining experiments to stop...')
+            worker_manager.wait_until_all_evaluations_are_done()
+            logger.info('BugHog has finished the evaluation!')
+            self.__update_state(is_running=False, status='idle', queue=self.eval_queue)
+
+    def run_single_evaluation(self, eval_params: EvaluationParameters, worker_manager: WorkerManager) -> None:
+        browser_name = eval_params.browser_configuration.browser_name
+        experiment_name = eval_params.evaluation_range.mech_group
+
+        logger.info(f"Starting evaluation for experiment '{experiment_name}' with browser '{browser_name}'")
+
+        search_strategy = self.create_sequence_strategy(eval_params)
+
+        try:
+            while (self.stop_gracefully or self.stop_forcefully) is False:
+                # Update search strategy with new potentially new results
+                current_state = search_strategy.next()
+
+                # Prepare worker parameters
+                worker_params = eval_params.create_worker_params_for(current_state, self.db_connection_params)
+
+                # Start worker to perform evaluation
+                worker_manager.start_test(worker_params)
+
+        except SequenceFinished:
+            logger.debug('Last experiment has started')
+            self.state['reason'] = 'finished'
+            self.__update_eval_queue(eval_params.evaluation_range.mech_group, 'done')
+
+    @staticmethod
+    def create_sequence_strategy(eval_params: EvaluationParameters) -> SequenceStrategy:
+        sequence_config = eval_params.sequence_configuration
+        search_strategy = sequence_config.search_strategy
+        sequence_limit = sequence_config.sequence_limit
+        outcome_checker = OutcomeChecker(sequence_config)
+        state_factory = StateFactory(eval_params, outcome_checker)
+
+        if search_strategy == 'bgb_sequence':
+            strategy = BiggestGapBisectionSequence(state_factory, sequence_limit)
+        elif search_strategy == 'bgb_search':
+            strategy = BiggestGapBisectionSearch(state_factory)
+        elif search_strategy == 'comp_search':
+            strategy = CompositeSearch(state_factory, sequence_limit)
         else:
-            major_version_range = None
-        if data.get("lower_revision_nb", None) and data.get("upper_revision_nb", None):
-            revision_number_range = (
-                data["lower_revision_nb"],
-                data["upper_revision_nb"],
-            )
+            raise AttributeError("Unknown search strategy option '%s'" % search_strategy)
+        return strategy
+
+    def activate_stop_gracefully(self):
+        if self.evaluation_framework:
+            self.stop_gracefully = True
+            self.__update_state(is_running=True, reason='user', status='waiting_to_stop')
+            self.evaluation_framework.stop_gracefully()
+            logger.info('Received user signal to gracefully stop.')
         else:
-            revision_number_range = None
-        return PlotParameters(
-            data.get("plot_mech_group"),
-            data.get("target_mech_id"),
-            data.get("browser_name"),
-            data.get("db_collection"),
-            major_version_range=major_version_range,
-            revision_number_range=revision_number_range,
-            browser_config=data.get("browser_setting", "default"),
-            extensions=data.get("extensions", []),
-            cli_options=data.get("cli_options", []),
-            dirty_allowed=data.get("dirty_allowed", True),
-            target_cookie_name=None
-            if data.get("check_for") == "request"
-            else data.get("target_cookie_name", "generic"),
-        )
-
-    @staticmethod
-    def get_data_sources(data: dict):
-        params = Main.convert_to_plotparams(data)
-
-        if PlotFactory.validate_params(params):
-            return None, None
-
-        return \
-            PlotFactory.get_plot_revision_data(params, MongoDB()), \
-            PlotFactory.get_plot_version_data(params, MongoDB())
-
-    @staticmethod
-    def get_poc(project: str, poc: str) -> dict:
-        return Main.master.evaluation_framework.get_poc_structure(project, poc)
-
-    @staticmethod
-    def get_poc_file(project: str, poc: str, domain: str, path: str, file: str) -> str:
-        return Main.master.evaluation_framework.get_poc_file(project, poc, domain, path, file)
-
-    @staticmethod
-    def update_poc_file(project: str, poc: str, domain: str, path: str, file: str, content: str) -> bool:
-        logger.debug(f'Updating file {file} of project {project} and poc {poc}')
-        return Main.master.evaluation_framework.update_poc_file(project, poc, domain, path, file, content)
-
-    @staticmethod
-    def create_empty_poc(project: str, poc_name: str) -> bool:
-        return Main.master.evaluation_framework.create_empty_poc(project, poc_name)
-
-    @staticmethod
-    def get_available_domains() -> list[str]:
-        return Global.get_available_domains()
-
-    @staticmethod
-    def add_page(project: str, poc: str, domain: str, path: str, file_type: str) -> bool:
-        return Main.master.evaluation_framework.add_page(project, poc, domain, path, file_type)
-
-    @staticmethod
-    def add_config(project: str, poc: str, type: str) -> bool:
-        return Main.master.evaluation_framework.add_config(project, poc, type)
-
-    @staticmethod
-    def sigint_handler(signum, frame):
-        return Main.master.stop_bughog()
+            logger.info('Received user signal to gracefully stop, but no evaluation is running.')
+
+    def activate_stop_forcefully(self) -> None:
+        if self.evaluation_framework:
+            self.stop_forcefully = True
+            self.__update_state(is_running=True, reason='user', status='waiting_to_stop')
+            self.evaluation_framework.stop_gracefully()
+            WorkerManager.forcefully_stop_all_running_containers()
+            logger.info('Received user signal to forcefully stop.')
+        else:
+            logger.info('Received user signal to forcefully stop, but no evaluation is running.')
+
+    def quit_bughog(self) -> None:
+        """
+        Quits the bughog application, stopping all associated containers.
+        """
+        logger.info('Stopping all running BugHog containers...')
+        self.activate_stop_forcefully()
+        mongodb_container.stop()
+        logger.info('Stopping BugHog core...')
+        exit(0)
+
+    def sigint_handler(self, sig_number, stack_frame) -> None:
+        logger.debug(f'Sigint received with number {sig_number} for stack frame {stack_frame}')
+        self.quit_bughog()
+
+    def push_info(self, ws, *args) -> None:
+        update = {}
+        all = 'all' in args
+        for arg in args:
+            if arg == 'db_info' or all:
+                update['db_info'] = MongoDB().get_info()
+            if arg == 'logs' or all:
+                update['logs'] = Loggers.get_logs()
+            if arg == 'state' or all:
+                update['state'] = self.state
+        Clients.push_info(ws, update)
+
+    def __update_state(self, **kwargs) -> None:
+        for key, value in kwargs.items():
+            self.state[key] = value
+        Clients.push_info_to_all({'state': self.state})
+
+    def __init_eval_queue(self, eval_params_list: list[EvaluationParameters]) -> None:
+        self.eval_queue = []
+        for eval_params in eval_params_list:
+            self.eval_queue.append({
+                'experiment': eval_params.evaluation_range.mech_group,
+                'state': 'pending'
+            })
+
+    def __update_eval_queue(self, experiment: str, state: str) -> None:
+        for eval in self.eval_queue:
+            if eval['experiment'] == experiment:
+                eval['state'] = state
+                return
diff --git a/bci/master.py b/bci/master.py
deleted file mode 100644
index 60b36ce5..00000000
--- a/bci/master.py
+++ /dev/null
@@ -1,169 +0,0 @@
-import logging
-
-import bci.database.mongo.container as mongodb_container
-from bci.configuration import Global
-from bci.database.mongo.mongodb import MongoDB, ServerException
-from bci.database.mongo.revision_cache import RevisionCache
-from bci.distribution.worker_manager import WorkerManager
-from bci.evaluations.custom.custom_evaluation import CustomEvaluationFramework
-from bci.evaluations.logic import (
-    DatabaseParameters,
-    EvaluationParameters,
-)
-from bci.evaluations.outcome_checker import OutcomeChecker
-from bci.search_strategy.bgb_search import BiggestGapBisectionSearch
-from bci.search_strategy.bgb_sequence import BiggestGapBisectionSequence
-from bci.search_strategy.composite_search import CompositeSearch
-from bci.search_strategy.sequence_strategy import SequenceFinished, SequenceStrategy
-from bci.version_control.factory import StateFactory
-from bci.version_control.states.revisions.firefox import BINARY_AVAILABILITY_MAPPING
-from bci.web.clients import Clients
-
-logger = logging.getLogger(__name__)
-
-
-class Master:
-    def __init__(self) -> None:
-        self.state = {'is_running': False, 'reason': 'init', 'status': 'idle'}
-
-        self.stop_gracefully = False
-        self.stop_forcefully = False
-
-        self.firefox_build = None
-        self.chromium_build = None
-
-        self.eval_queue = []
-
-        Global.initialize_folders()
-        self.db_connection_params = Global.get_database_params()
-        self.connect_to_database(self.db_connection_params)
-        RevisionCache.store_firefox_binary_availability(BINARY_AVAILABILITY_MAPPING)  # TODO: find better place
-        self.evaluation_framework = CustomEvaluationFramework()
-        logger.info('BugHog is ready!')
-
-    def connect_to_database(self, db_connection_params: DatabaseParameters) -> None:
-        try:
-            MongoDB().connect(db_connection_params)
-        except ServerException:
-            logger.error('Could not connect to database.', exc_info=True)
-
-    def run(self, eval_params_list: list[EvaluationParameters]) -> None:
-        # Sequence_configuration settings are the same over evaluation parameters (quick fix)
-        worker_manager = WorkerManager(eval_params_list[0].sequence_configuration.nb_of_containers)
-        self.stop_gracefully = False
-        self.stop_forcefully = False
-        try:
-            self.__init_eval_queue(eval_params_list)
-            for eval_params in eval_params_list:
-                if self.stop_gracefully or self.stop_forcefully:
-                    break
-                self.__update_eval_queue(eval_params.evaluation_range.mech_group, 'active')
-                self.__update_state(is_running=True,reason='user', status='running', queue=self.eval_queue)
-                self.run_single_evaluation(eval_params, worker_manager)
-
-        except Exception as e:
-            logger.critical('A critical error occurred', exc_info=True)
-            raise e
-        finally:
-            # Gracefully exit
-            if self.stop_gracefully:
-                logger.info('Gracefully stopping experiment queue due to user end signal...')
-                self.state['reason'] = 'user'
-            if self.stop_forcefully:
-                logger.info('Forcefully stopping experiment queue due to user end signal...')
-                self.state['reason'] = 'user'
-                worker_manager.forcefully_stop_all_running_containers()
-            else:
-                logger.info('Gracefully stopping experiment queue since last experiment started.')
-            # MongoDB.disconnect()
-            logger.info('Waiting for remaining experiments to stop...')
-            worker_manager.wait_until_all_evaluations_are_done()
-            logger.info('BugHog has finished the evaluation!')
-            self.__update_state(is_running=False, status='idle', queue=self.eval_queue)
-
-    def run_single_evaluation(self, eval_params: EvaluationParameters, worker_manager: WorkerManager) -> None:
-        browser_name = eval_params.browser_configuration.browser_name
-        experiment_name = eval_params.evaluation_range.mech_group
-
-        logger.info(f"Starting evaluation for experiment '{experiment_name}' with browser '{browser_name}'")
-
-        search_strategy = self.create_sequence_strategy(eval_params)
-
-        try:
-            while (self.stop_gracefully or self.stop_forcefully) is False:
-                # Update search strategy with new potentially new results
-                current_state = search_strategy.next()
-
-                # Prepare worker parameters
-                worker_params = eval_params.create_worker_params_for(current_state, self.db_connection_params)
-
-                # Start worker to perform evaluation
-                worker_manager.start_test(worker_params)
-
-        except SequenceFinished:
-            logger.debug('Last experiment has started')
-            self.state['reason'] = 'finished'
-            self.__update_eval_queue(eval_params.evaluation_range.mech_group, 'done')
-
-    @staticmethod
-    def create_sequence_strategy(eval_params: EvaluationParameters) -> SequenceStrategy:
-        sequence_config = eval_params.sequence_configuration
-        search_strategy = sequence_config.search_strategy
-        sequence_limit = sequence_config.sequence_limit
-        outcome_checker = OutcomeChecker(sequence_config)
-        state_factory = StateFactory(eval_params, outcome_checker)
-
-        if search_strategy == 'bgb_sequence':
-            strategy = BiggestGapBisectionSequence(state_factory, sequence_limit)
-        elif search_strategy == 'bgb_search':
-            strategy = BiggestGapBisectionSearch(state_factory)
-        elif search_strategy == 'comp_search':
-            strategy = CompositeSearch(state_factory, sequence_limit)
-        else:
-            raise AttributeError("Unknown search strategy option '%s'" % search_strategy)
-        return strategy
-
-    def activate_stop_gracefully(self):
-        if self.evaluation_framework:
-            self.stop_gracefully = True
-            self.__update_state(is_running=True, reason='user', status='waiting_to_stop')
-            self.evaluation_framework.stop_gracefully()
-            logger.info('Received user signal to gracefully stop.')
-        else:
-            logger.info('Received user signal to gracefully stop, but no evaluation is running.')
-
-    def activate_stop_forcefully(self) -> None:
-        if self.evaluation_framework:
-            self.stop_forcefully = True
-            self.__update_state(is_running=True, reason='user', status='waiting_to_stop')
-            self.evaluation_framework.stop_gracefully()
-            WorkerManager.forcefully_stop_all_running_containers()
-            logger.info('Received user signal to forcefully stop.')
-        else:
-            logger.info('Received user signal to forcefully stop, but no evaluation is running.')
-
-    def stop_bughog(self) -> None:
-        logger.info('Stopping all running BugHog containers...')
-        self.activate_stop_forcefully()
-        mongodb_container.stop()
-        logger.info('Stopping BugHog core...')
-        exit(0)
-
-    def __update_state(self, **kwargs) -> None:
-        for key, value in kwargs.items():
-            self.state[key] = value
-        Clients.push_info_to_all('state')
-
-    def __init_eval_queue(self, eval_params_list: list[EvaluationParameters]) -> None:
-        self.eval_queue = []
-        for eval_params in eval_params_list:
-            self.eval_queue.append({
-                'experiment': eval_params.evaluation_range.mech_group,
-                'state': 'pending'
-            })
-
-    def __update_eval_queue(self, experiment: str, state: str) -> None:
-        for eval in self.eval_queue:
-            if eval['experiment'] == experiment:
-                eval['state'] = state
-                return
diff --git a/bci/web/blueprints/api.py b/bci/web/blueprints/api.py
index 0b901d4a..3a4468f9 100644
--- a/bci/web/blueprints/api.py
+++ b/bci/web/blueprints/api.py
@@ -3,11 +3,15 @@
 import os
 import threading
 
-from flask import Blueprint, request
+from flask import Blueprint, current_app, request
 
+import bci.browser.support as browser_support
+import bci.evaluations.logic as application_logic
+from bci.analysis.plot_factory import PlotFactory
 from bci.app import sock
-from bci.evaluations.logic import evaluation_factory
-from bci.main import Main as bci_api
+from bci.configuration import Global, Loggers
+from bci.evaluations.logic import PlotParameters
+from bci.main import Main
 from bci.web.clients import Clients
 
 logger = logging.getLogger(__name__)
@@ -28,14 +32,24 @@ def __start_thread(func, args=None) -> bool:
         return True
 
 
+def __get_main() -> Main:
+    if main := current_app.config['main']:
+        return main
+    raise Exception('Main object is not instantiated')
+
+
 @api.before_request
 def check_readiness():
-    if not bci_api.is_ready():
+    try:
+        pass
+        # _ = ____get_main()
+    except Exception as e:
+        logger.critical(e)
         return {
             'status': 'NOK',
             'msg': 'BugHog is not ready',
             'info': {
-                'log': bci_api.get_logs(),
+                'log': Loggers.get_logs()
             }
         }
 
@@ -63,8 +77,8 @@ def start_evaluation():
         }
 
     data = request.json.copy()
-    params = evaluation_factory(data)
-    if __start_thread(bci_api.run, args=[params]):
+    params = application_logic.evaluation_factory(data)
+    if __start_thread(__get_main().run, args=[params]):
         return {
             'status': 'OK'
         }
@@ -85,9 +99,9 @@ def stop_evaluation():
     data = request.json.copy()
     forcefully = data.get('forcefully', False)
     if forcefully:
-        bci_api.stop_forcefully()
+        __get_main().activate_stop_forcefully()
     else:
-        bci_api.stop_gracefully()
+        __get_main().activate_stop_gracefully()
     return {
         'status': 'OK'
     }
@@ -113,7 +127,7 @@ def init_websocket(ws):
             if params := message.get('select_project', None):
                 Clients.associate_project(ws, params)
             if requested_variables := message.get('get', []):
-                Clients.push_info(ws, *requested_variables)
+                __get_main().push_info(ws, *requested_variables)
         except ValueError:
             logger.warning('Ignoring invalid message from client.')
     ws.send('Connected to BugHog')
@@ -123,7 +137,7 @@ def init_websocket(ws):
 def get_browsers():
     return {
         'status': 'OK',
-        'browsers': bci_api.get_browser_support()
+        'browsers': [browser_support.get_chromium_support(), browser_support.get_firefox_support()]
     }
 
 
@@ -131,7 +145,7 @@ def get_browsers():
 def get_projects():
     return {
         'status': 'OK',
-        'projects': bci_api.get_projects_of_custom_framework()
+        'projects': __get_main().evaluation_framework.get_projects()
     }
 
 
@@ -145,7 +159,7 @@ def create_project():
     project_name = request.json.get('project_name')
     return {
         'status': 'OK',
-        'projects': bci_api.create_empty_project(project_name)
+        'projects': __get_main().evaluation_framework.create_empty_project(project_name)
     }
 
 
@@ -174,23 +188,21 @@ def data_source():
         }
 
     params = request.json.copy()
-    revision_data, version_data = bci_api.get_data_sources(params)
-    if revision_data or version_data:
-        return {
-            'status': 'OK',
-            'revision': revision_data,
-            'version': version_data
-        }
-    else:
+    plot_params = PlotParameters.from_dict(params)
+    if missing_params := PlotFactory.validate_params(plot_params):
         return {
             'status': 'NOK',
-            'msg': 'Invalid type'
+            'msg': f'Missing plot parameters: {missing_params}'
+        }
+    return {
+            'status': 'OK',
+            'revision': PlotFactory.get_plot_revision_data(params),
+            'version': PlotFactory.get_plot_version_data(params)
         }
-
 
 @api.route('/poc/<string:project>/', methods=['GET'])
 def get_experiments(project: str):
-    experiments = bci_api.get_mech_groups_of_evaluation_framework('custom', project)
+    experiments = __get_main().evaluation_framework.get_mech_groups(project)
     return {
         'status': 'OK',
         'experiments': experiments
@@ -201,7 +213,7 @@ def get_experiments(project: str):
 def poc(project: str, poc: str):
     return {
         'status': 'OK',
-        'tree': bci_api.get_poc(project, poc)
+        'tree': __get_main().evaluation_framework.get_poc_structure(project, poc)
     }
 
 
@@ -212,7 +224,7 @@ def get_poc_file_content(project: str, poc: str, file: str):
     if request.method == 'GET':
         return {
             'status': 'OK',
-            'content': bci_api.get_poc_file(project, poc, domain, path, file)
+            'content': __get_main().evaluation_framework.get_poc_file(project, poc, domain, path, file)
         }
     else:
         if not request.json:
@@ -221,7 +233,8 @@ def get_poc_file_content(project: str, poc: str, file: str):
                 'msg': 'No content to update file with'
             }
         data = request.json.copy()
-        success = bci_api.update_poc_file(project, poc, domain, path, file, data['content'])
+        content = data['content']
+        success = __get_main().evaluation_framework.update_poc_file(project, poc, domain, path, file, content)
         if success:
             return {
                 'status': 'OK'
@@ -241,7 +254,10 @@ def add_page(project: str, poc: str):
         }
 
     data = request.json.copy()
-    success = bci_api.add_page(project, poc, data['domain'], data['page'], data['file_type'])
+    domain = data['domain']
+    path = data['page']
+    file_type = data['file_type']
+    success = __get_main().evaluation_framework.add_page(project, poc, domain, path, file_type)
     if success:
         return {
             'status': 'OK'
@@ -260,7 +276,8 @@ def add_config(project: str, poc: str):
             'msg': "No parameters found"
         }
     data = request.json.copy()
-    success = bci_api.add_config(project, poc, data['type'])
+    type = data['type']
+    success = __get_main().evaluation_framework.add_config(project, poc, type)
     if success:
         return {
             'status': 'OK'
@@ -275,7 +292,7 @@ def add_config(project: str, poc: str):
 def get_available_domains():
     return {
         'status': 'OK',
-        'domains': bci_api.get_available_domains()
+        'domains': Global.get_available_domains()
     }
 
 
@@ -293,7 +310,8 @@ def create_experiment(project: str):
             'status': 'NOK',
             'msg': 'Missing experiment name'
         }
-    if bci_api.create_empty_poc(project, data['poc_name']):
+    poc_name = data['poc_name']
+    if __get_main().evaluation_framework.create_empty_poc(project, poc_name):
         return {
             'status': 'OK'
         }
diff --git a/bci/web/clients.py b/bci/web/clients.py
index 9dad0fd8..acb2045b 100644
--- a/bci/web/clients.py
+++ b/bci/web/clients.py
@@ -2,8 +2,12 @@
 import threading
 from venv import logger
 
+from flask import current_app
 from simple_websocket import Server
 
+from bci.analysis.plot_factory import PlotFactory
+from bci.evaluations.logic import PlotParameters
+
 
 class Clients:
     __semaphore = threading.Semaphore()
@@ -40,10 +44,17 @@ def associate_project(ws_client: Server, project: str):
 
     @staticmethod
     def push_results(ws_client: Server):
-        from bci.main import Main as bci_api
-
         if params := Clients.__clients.get(ws_client, None):
-            revision_data, version_data = bci_api.get_data_sources(params)
+            plot_params = PlotParameters.from_dict(params)
+
+            if PlotFactory.validate_params(plot_params):
+                revision_data = None
+                version_data = None
+            else:
+                revision_data = PlotFactory.get_plot_revision_data(plot_params)
+                version_data = PlotFactory.get_plot_version_data(plot_params)
+
+
             ws_client.send(
                 json.dumps(
                     {
@@ -64,29 +75,17 @@ def push_results_to_all():
             Clients.push_results(ws_client)
 
     @staticmethod
-    def push_info(ws_client: Server, *requested_vars: str):
-        from bci.main import Main as bci_api
-
-        update = {}
-        all = not requested_vars or 'all' in requested_vars
-        if 'db_info' in requested_vars or all:
-            update['db_info'] = bci_api.get_database_info()
-        if 'logs' in requested_vars or all:
-            update['logs'] = bci_api.get_logs()
-        if 'state' in requested_vars or all:
-            update['state'] = bci_api.get_state()
+    def push_info(ws_client: Server, update: dict):
         ws_client.send(json.dumps({'update': update}))
 
     @staticmethod
-    def push_info_to_all(*requested_vars: str):
+    def push_info_to_all(update: dict):
         Clients.__remove_disconnected_clients()
         for ws_client in Clients.__clients.keys():
-            Clients.push_info(ws_client, *requested_vars)
+            Clients.push_info(ws_client, update)
 
     @staticmethod
     def push_experiments(ws_client: Server):
-        from bci.main import Main as bci_api
-
         client_info = Clients.__clients[ws_client]
         if client_info is None:
             logger.error('Could not find any associated info for this client')
@@ -94,7 +93,9 @@ def push_experiments(ws_client: Server):
 
         project = client_info.get('project', None)
         if project:
-            experiments = bci_api.get_mech_groups_of_evaluation_framework('custom', project)
+            from bci.main import Main
+            main: Main = current_app.config['main']
+            experiments = main.evaluation_framework.get_mech_groups(project)
             ws_client.send(json.dumps({'update': {'experiments': experiments}}))
 
     @staticmethod
diff --git a/bci/web/vue/src/App.vue b/bci/web/vue/src/App.vue
index b2b56a18..2ca833a7 100644
--- a/bci/web/vue/src/App.vue
+++ b/bci/web/vue/src/App.vue
@@ -183,7 +183,8 @@ export default {
   created: function () {
     this.websocket = this.create_socket();
     this.get_projects();
-    this.get_browser_support();const path = `/api/poc/domain/`;
+    this.get_browser_support();
+    const path = `/api/poc/domain/`;
     axios.get(path)
     .then((res) => {
       if (res.data.status === "OK") {
diff --git a/bci/web/vue/src/components/poc-editor.vue b/bci/web/vue/src/components/poc-editor.vue
index 14bb2ef7..98385d7a 100644
--- a/bci/web/vue/src/components/poc-editor.vue
+++ b/bci/web/vue/src/components/poc-editor.vue
@@ -286,7 +286,6 @@
         this.active_poc.name = null;
         this.active_poc.active_domain = null;
         this.active_poc.active_path = null;
-        this.update_poc_tree(val);
       },
     },
   };

From 7572c704b5a611ccc3d32d2c9386484f621df9f8 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Tue, 26 Nov 2024 11:59:42 +0000
Subject: [PATCH 49/57] Add option to remove datapoints by SHIFT clicking
 squares and dots in the Gantt chart

---
 bci/database/mongo/mongodb.py                 |  5 ++
 bci/evaluations/logic.py                      | 10 +++
 bci/main.py                                   |  5 ++
 bci/web/blueprints/api.py                     | 14 ++++
 bci/web/vue/src/App.vue                       |  6 +-
 bci/web/vue/src/components/gantt.vue          | 65 +++++++++++++++++--
 bci/web/vue/src/components/section-header.vue |  2 +-
 7 files changed, 97 insertions(+), 10 deletions(-)

diff --git a/bci/database/mongo/mongodb.py b/bci/database/mongo/mongodb.py
index 6351e79c..df8c5678 100644
--- a/bci/database/mongo/mongodb.py
+++ b/bci/database/mongo/mongodb.py
@@ -339,6 +339,11 @@ def get_documents_for_plotting(self, params: PlotParameters, releases: bool = Fa
         )
         return list(docs)
 
+    def remove_datapoint(self, params: TestParameters) -> None:
+        collection = self.get_collection(params.database_collection)
+        query = self.__to_query(params)
+        collection.delete_one(query)
+
     def get_info(self) -> dict:
         if self.client and self.client.address:
             return {'type': 'mongo', 'host': self.client.address[0], 'connected': True}
diff --git a/bci/evaluations/logic.py b/bci/evaluations/logic.py
index 8c1cbe36..3097c592 100644
--- a/bci/evaluations/logic.py
+++ b/bci/evaluations/logic.py
@@ -190,6 +190,16 @@ class TestParameters:
     def create_test_result_with(self, browser_version: str, binary_origin: str, data: dict, dirty: bool) -> TestResult:
         return TestResult(self, browser_version, binary_origin, data, dirty)
 
+    @staticmethod
+    def from_dict(data) -> Optional[TestParameters]:
+        if data is None:
+            return None
+        browser_configuration = BrowserConfiguration.from_dict(data)
+        evaluation_configuration = EvaluationConfiguration.from_dict(data)
+        state = State.from_dict(data)
+        mech_group = data['mech_group']
+        database_collection = data['db_collection']
+        return TestParameters(browser_configuration, evaluation_configuration, state, mech_group, database_collection)
 
 @dataclass(frozen=True)
 class TestResult:
diff --git a/bci/main.py b/bci/main.py
index 0c27412e..a377f18b 100644
--- a/bci/main.py
+++ b/bci/main.py
@@ -9,6 +9,7 @@
 from bci.evaluations.logic import (
     DatabaseParameters,
     EvaluationParameters,
+    TestParameters,
 )
 from bci.evaluations.outcome_checker import OutcomeChecker
 from bci.search_strategy.bgb_search import BiggestGapBisectionSearch
@@ -168,6 +169,10 @@ def push_info(self, ws, *args) -> None:
                 update['state'] = self.state
         Clients.push_info(ws, update)
 
+    def remove_datapoint(self, params: TestParameters) -> None:
+        MongoDB().remove_datapoint(params)
+        Clients.push_results_to_all()
+
     def __update_state(self, **kwargs) -> None:
         for key, value in kwargs.items():
             self.state[key] = value
diff --git a/bci/web/blueprints/api.py b/bci/web/blueprints/api.py
index 3a4468f9..607edcfe 100644
--- a/bci/web/blueprints/api.py
+++ b/bci/web/blueprints/api.py
@@ -320,3 +320,17 @@ def create_experiment(project: str):
             'status': 'NOK',
             'msg': 'Could not create experiment'
         }
+
+
+@api.route('/data/remove/', methods=['POST'])
+def remove_datapoint():
+    if (params := application_logic.TestParameters.from_dict(request.json)) is None:
+        return {
+            'status': 'NOK',
+            'msg': "No parameters found"
+        }
+    __get_main().remove_datapoint(params)
+    return {
+        'status': 'OK'
+    }
+
diff --git a/bci/web/vue/src/App.vue b/bci/web/vue/src/App.vue
index 2ca833a7..4d316bf0 100644
--- a/bci/web/vue/src/App.vue
+++ b/bci/web/vue/src/App.vue
@@ -239,8 +239,8 @@ export default {
         }
         this.propagate_new_params();
       });
-      websocket.addEventListener("message", () => {
-        const data = JSON.parse(event.data);
+      websocket.addEventListener("message", (e) => {
+        const data = JSON.parse(e.data);
         if (data.hasOwnProperty("update")) {
           if (data.update.hasOwnProperty("plot_data")) {
             const revision_data = data.update.plot_data.revision_data;
@@ -553,7 +553,7 @@ export default {
             </ul>
           </div>
         </div>
-        <gantt ref="gantt"></gantt>
+        <gantt ref="gantt" :eval_params="this.eval_params"></gantt>
       </div>
     </div>
 
diff --git a/bci/web/vue/src/components/gantt.vue b/bci/web/vue/src/components/gantt.vue
index a23bf780..a31ae987 100644
--- a/bci/web/vue/src/components/gantt.vue
+++ b/bci/web/vue/src/components/gantt.vue
@@ -1,8 +1,14 @@
 <script>
+import axios from 'axios'
 export default {
+    props: {
+      eval_params: Object,
+    },
     data() {
         return {
             browser_name: null,
+            poc: null,
+            project: null,
             plot: null,
             revision_source: {
                 data: [],
@@ -18,6 +24,17 @@ export default {
     methods: {
         init_plot() {
             console.log("Initializing Gantt chart...");
+            
+            document.addEventListener("keydown", (e) => {
+                if (e.shiftKey) {
+                    this.shift_down = true;
+                }
+            });
+            document.addEventListener("keyup", (e) => {
+                if (e.shiftKey) {
+                    this.shift_down = false;
+                }
+            });
 
             if (this.revision_source.length === 0 || this.version_source.length === 0) {
                 this.x_min = 1;
@@ -91,11 +108,29 @@ export default {
             if (urlTemplate) {
                 const tapTool = new Bokeh.TapTool({
                     behavior: 'select',
-                    callback: () => {
-                        if (this.revision_source.selected.indices.length > 0) {
-                            let index = this.revision_source.selected.indices[0];
-                            let revision_number = this.revision_source.data.revision_number[index];
-                            window.open(urlTemplate + revision_number);
+                    callback: (e) => {
+                        var index;
+                        if ((index = this.revision_source.selected.indices[0]) !== undefined) {
+                            var revision_number = this.revision_source.data.revision_number[index];
+                            var browser_version = this.revision_source.data.browser_version[index];
+                            var type = "revision";
+                        } else if ((index = this.version_source.selected.indices[0]) !== undefined) {
+                            var revision_number = this.version_source.data.revision_number[index];
+                            var browser_version = this.version_source.data.browser_version[index];
+                            var type = "version";
+                        } else {
+                            console.log("Nothing interesting was selected...");
+                            return;
+                        }
+
+                        if (this.shift_down) {
+                            // Ask to remove datapoint
+                            this.remove_datapoint(revision_number, browser_version, type);
+                        } else {
+                            // Open revision page
+                            if (this.revision_source.selected.indices.length > 0) {
+                                window.open(urlTemplate + revision_number);
+                            }
                         }
                         this.revision_source.selected.indices = [];
                         this.version_source.selected.indices = [];
@@ -122,13 +157,15 @@ export default {
             Bokeh.Plotting.show(this.plot, document.getElementById('gantt'));
             console.log("Gantt chart initialized!");
         },
-        update_plot(browser_name, revision_data, version_data) {
+        update_plot(browser_name, revision_data, version_data, project, poc) {
             if (revision_data === null && version_data === null) {
                 return;
             }
 
             let init_required = this.revision_source === null || this.browser_name !== browser_name;
             this.browser_name = browser_name;
+            this.project = project;
+            this.poc = poc;
 
             if (init_required) {
                 this.revision_source = new Bokeh.ColumnDataSource({ data: revision_data });;
@@ -161,6 +198,22 @@ export default {
                 }
             }
         },
+        remove_datapoint(revision_number, browser_version, type) {
+            console.log("Removing datapoint ", revision_number, type);
+            const path = "/api/data/remove/"
+            var params = this.eval_params
+            params['type'] = type
+            params["revision_number"] = revision_number
+            params["major_version"] = browser_version
+            params["mech_group"] = params["plot_mech_group"]
+            axios.post(path, params)
+            .then((res) => {
+            })
+            .catch((error) => {
+                console.error(error);
+            });
+
+        },
     },
 };
 </script>
diff --git a/bci/web/vue/src/components/section-header.vue b/bci/web/vue/src/components/section-header.vue
index 0cd95c7d..1740b38a 100644
--- a/bci/web/vue/src/components/section-header.vue
+++ b/bci/web/vue/src/components/section-header.vue
@@ -42,7 +42,7 @@
           },
           "results": {
             "title": "Results",
-            "tooltip": "Choose an experiment from the dropdown menu to visualize its results in the Gantt chart below. Squares represent (approximate) release binaries, while dots represent revision binaries. Clicking on a dot will open the web page for the associated revision in the public browser repository."
+            "tooltip": "Choose an experiment from the dropdown menu to visualize its results in the Gantt chart below. Squares represent (approximate) release binaries, while dots represent revision binaries. Clicking on a dot will open the web page for the associated revision in the public browser repository. Holding shift while clicking on any dot or square will delete the particular result."
           },
           "search_strategy": {
             "title": "Search strategy",

From c00eb5bb75707beb02cc91ba855f16bf733faade Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Tue, 26 Nov 2024 17:30:40 +0000
Subject: [PATCH 50/57] Fix SHIFT down checking for Gantt chart

---
 bci/web/vue/src/components/gantt.vue | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bci/web/vue/src/components/gantt.vue b/bci/web/vue/src/components/gantt.vue
index a31ae987..fcbad9d4 100644
--- a/bci/web/vue/src/components/gantt.vue
+++ b/bci/web/vue/src/components/gantt.vue
@@ -19,12 +19,13 @@ export default {
             revision_range: null,
             x_min: null,
             x_max: null,
+            shift_down: false,
         }
     },
     methods: {
         init_plot() {
             console.log("Initializing Gantt chart...");
-            
+
             document.addEventListener("keydown", (e) => {
                 if (e.shiftKey) {
                     this.shift_down = true;
@@ -123,7 +124,7 @@ export default {
                             return;
                         }
 
-                        if (this.shift_down) {
+                        if (this.shift_down === true) {
                             // Ask to remove datapoint
                             this.remove_datapoint(revision_number, browser_version, type);
                         } else {

From fd30b0b606ec3fb6ca0682a42e1dc5975d6d51ad Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Tue, 26 Nov 2024 17:39:07 +0000
Subject: [PATCH 51/57] Isolate browser sessions and clean Downloads folder
 between tries.

Additionally, fix bug where cached Firefox binary data was misinterpreted.
---
 bci/browser/configuration/browser.py          | 13 +++++++++++-
 bci/browser/configuration/firefox.py          |  2 +-
 bci/browser/configuration/profile.py          | 16 ++++++++++-----
 bci/database/mongo/revision_cache.py          |  2 +-
 bci/evaluations/custom/custom_evaluation.py   | 20 +++++++++----------
 bci/util.py                                   | 10 ++++++++++
 .../states/revisions/firefox.py               |  2 ++
 7 files changed, 46 insertions(+), 19 deletions(-)

diff --git a/bci/browser/configuration/browser.py b/bci/browser/configuration/browser.py
index f6a9f2e7..6b0c86df 100644
--- a/bci/browser/configuration/browser.py
+++ b/bci/browser/configuration/browser.py
@@ -63,11 +63,16 @@ def post_evaluation_cleanup(self):
 
     def pre_test_setup(self):
         self.__prepare_execution_folder()
-        self._prepare_profile_folder()
 
     def post_test_cleanup(self):
         self.__remove_execution_folder()
+
+    def pre_try_setup(self):
+        self._prepare_profile_folder()
+
+    def post_try_cleanup(self):
         self.__remove_profile_folder()
+        self.__empty_downloads_folder()
 
     def __fetch_binary(self):
         self.binary.fetch_binary()
@@ -87,9 +92,15 @@ def __remove_execution_folder(self):
         util.rmtree(self.__get_execution_folder_path())
 
     def __remove_profile_folder(self):
+        if self._profile_path is None:
+            return
         remove_profile_execution_folder(self._profile_path)
         self._profile_path = None
 
+    def __empty_downloads_folder(self):
+        download_folder = '/root/Downloads'
+        util.remove_all_in_folder(download_folder)
+
     def __get_execution_folder_path(self) -> str:
         return os.path.join(EXECUTION_PARENT_FOLDER, str(self.state.name))
 
diff --git a/bci/browser/configuration/firefox.py b/bci/browser/configuration/firefox.py
index cff1d7f1..239934ab 100644
--- a/bci/browser/configuration/firefox.py
+++ b/bci/browser/configuration/firefox.py
@@ -96,7 +96,7 @@ def _prepare_profile_folder(self):
         if 'tp' in self.browser_config.browser_setting:
             self._profile_path = prepare_firefox_profile('tp-67')
         else:
-            self._profile_path = prepare_firefox_profile('default-67')
+            self._profile_path = prepare_firefox_profile()
 
         # Make Firefox trust the bughog CA
 
diff --git a/bci/browser/configuration/profile.py b/bci/browser/configuration/profile.py
index 520b612d..79e03d12 100644
--- a/bci/browser/configuration/profile.py
+++ b/bci/browser/configuration/profile.py
@@ -1,4 +1,5 @@
 import os
+from typing import Optional
 
 from bci import cli
 
@@ -6,7 +7,7 @@
 PROFILE_EXECUTION_FOLDER = '/tmp/profiles'
 
 
-def prepare_chromium_profile(profile_name: str = None) -> str:
+def prepare_chromium_profile(profile_name: Optional[str] = None) -> str:
     # Create new execution profile folder
     profile_execution_path = os.path.join(PROFILE_EXECUTION_FOLDER, 'new_profile')
     profile_execution_path = __create_folder(profile_execution_path)
@@ -14,21 +15,26 @@ def prepare_chromium_profile(profile_name: str = None) -> str:
     # Copy profile from storage to execution folder if profile_name is given
     if profile_name:
         if not os.path.exists(os.path.join(PROFILE_STORAGE_FOLDER, 'chromium', profile_name)):
-            raise Exception(f'Profile \'{profile_name}\' does not exist')
+            raise Exception(f"Profile '{profile_name}' does not exist")
         profile_storage_path = os.path.join(PROFILE_STORAGE_FOLDER, profile_name, 'Default')
         cli.execute(f'cp -r {profile_storage_path} {profile_execution_path}')
     return profile_execution_path
 
 
-def prepare_firefox_profile(profile_name: str = None) -> str:
+def prepare_firefox_profile(profile_name: Optional[str] = None) -> str:
+    """"
+    Create a temporary profile folder, based on the provided name of the premade profile.
+
+    :param profile_name: Reference to the premade profile folder used for creating the temporary profile.
+    """
     # Create new execution profile folder
     profile_execution_path = os.path.join(PROFILE_EXECUTION_FOLDER, 'new_profile')
     profile_execution_path = __create_folder(profile_execution_path)
 
     # Copy profile from storage to execution folder if profile_name is given
-    if profile_name is None:
+    if profile_name is not None:
         if not os.path.exists(os.path.join(PROFILE_STORAGE_FOLDER, 'firefox', profile_name)):
-            raise Exception(f'Profile \'{profile_name}\' does not exist')
+            raise Exception(f"Profile '{profile_name}' does not exist")
         profile_storage_path = os.path.join(PROFILE_STORAGE_FOLDER, profile_name)
         cli.execute(f'cp -r {profile_storage_path} {profile_execution_path}')
     return profile_execution_path
diff --git a/bci/database/mongo/revision_cache.py b/bci/database/mongo/revision_cache.py
index 08cb5d48..6a06efda 100644
--- a/bci/database/mongo/revision_cache.py
+++ b/bci/database/mongo/revision_cache.py
@@ -44,7 +44,7 @@ def firefox_has_binary_for(revision_nb: Optional[int], revision_id: Optional[str
     @staticmethod
     def firefox_get_binary_info(revision_id: str) -> Optional[dict]:
         collection = MongoDB().get_collection('firefox_binary_availability')
-        return collection.find_one({'revision_id': revision_id}, {'files_url': 1, 'app_version': 1})
+        return collection.find_one({'node': revision_id}, {'files_url': 1, 'app_version': 1})
 
     @staticmethod
     def firefox_get_previous_and_next_revision_nb_with_binary(revision_nb: int) -> tuple[Optional[int], Optional[int]]:
diff --git a/bci/evaluations/custom/custom_evaluation.py b/bci/evaluations/custom/custom_evaluation.py
index 55df01c8..96a441ba 100644
--- a/bci/evaluations/custom/custom_evaluation.py
+++ b/bci/evaluations/custom/custom_evaluation.py
@@ -123,24 +123,22 @@ def perform_specific_evaluation(self, browser: Browser, params: TestParameters)
             experiment = self.tests_per_project[params.evaluation_configuration.project][params.mech_group]
 
             max_tries = 3
-            if 'script' in experiment:
-                interaction = Interaction(browser, experiment['script'], params)
-                tries = 0
-                while tries < max_tries:
-                    tries += 1
+            for _ in range(max_tries):
+                browser.pre_try_setup()
+                if 'script' in experiment:
+                    interaction = Interaction(browser, experiment['script'], params)
                     interaction.execute()
-            else:
-                url_queue = experiment['url_queue']
-                for url in url_queue:
-                    tries = 0
-                    while tries < max_tries:
-                        tries += 1
+                else:
+                    url_queue = experiment['url_queue']
+                    for url in url_queue:
                         browser.visit(url)
+                browser.post_try_cleanup()
         except Exception as e:
             logger.error(f'Error during test: {e}', exc_info=True)
             is_dirty = True
         finally:
             collector.stop()
+
             results = collector.collect_results()
             if not is_dirty:
                 # New way to perform sanity check
diff --git a/bci/util.py b/bci/util.py
index ffaf9651..3175ca1c 100644
--- a/bci/util.py
+++ b/bci/util.py
@@ -42,6 +42,16 @@ def copy_folder(src_path, dst_path):
     shutil.copytree(src_path, dst_path, dirs_exist_ok=True)
 
 
+def remove_all_in_folder(folder_path: str) -> None:
+    for root, dirs, files in os.walk(folder_path):
+        for file_name in files:
+            file_path = os.path.join(root, file_name)
+            os.remove(file_path)
+        for dir_name in dirs:
+            dir_path = os.path.join(root, dir_name)
+            shutil.rmtree(dir_path)
+
+
 def rmtree(src_path):
     """
     Removes folder at given src_path.
diff --git a/bci/version_control/states/revisions/firefox.py b/bci/version_control/states/revisions/firefox.py
index f9eb8315..928864b5 100644
--- a/bci/version_control/states/revisions/firefox.py
+++ b/bci/version_control/states/revisions/firefox.py
@@ -28,6 +28,8 @@ def has_online_binary(self) -> bool:
 
     def get_online_binary_url(self) -> str:
         result = RevisionCache.firefox_get_binary_info(self._revision_id)
+        if result is None:
+            raise AttributeError(f"Could not find binary url for '{self._revision_id}")
         binary_base_url = result['files_url']
         app_version = result['app_version']
         binary_url = f'{binary_base_url}firefox-{app_version}.en-US.linux-x86_64.tar.bz2'

From 1cdecf738a6b43ad4bafa858eafa9bc94f9885ca Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Thu, 28 Nov 2024 08:58:57 +0000
Subject: [PATCH 52/57] Fix bug where states would be evaluated more than once

Because BGB Search was not aware of states that were already in progress when BGB Sequence had finished (no database entry yet), some states would be evaluated more than once on occasion.
This especially happened when there are more concurrent containers than states to evaluate.
---
 bci/search_strategy/bgb_search.py        | 16 ++++++++++++++--
 bci/search_strategy/bgb_sequence.py      |  5 +++--
 bci/search_strategy/composite_search.py  | 13 ++++++++-----
 bci/search_strategy/sequence_strategy.py |  5 +++--
 4 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/bci/search_strategy/bgb_search.py b/bci/search_strategy/bgb_search.py
index a9f6a221..34fcf674 100644
--- a/bci/search_strategy/bgb_search.py
+++ b/bci/search_strategy/bgb_search.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 from typing import Optional
 
@@ -16,13 +18,14 @@ class BiggestGapBisectionSearch(BiggestGapBisectionSequence):
     It stops when there are no more states to evaluate between two states with different outcomes.
     """
 
-    def __init__(self, state_factory: StateFactory) -> None:
+    def __init__(self, state_factory: StateFactory, completed_states: Optional[list[State]]=None) -> None:
         """
         Initializes the search strategy.
 
         :param state_factory: The factory to create new states.
+        :param completed_states: States that have already been returned.
         """
-        super().__init__(state_factory, 0)
+        super().__init__(state_factory, 0, completed_states=completed_states)
 
     def next(self) -> State:
         """
@@ -86,3 +89,12 @@ def __get_next_pair_to_split(self) -> Optional[tuple[State, State]]:
         # splitter of the second gap with having to wait for the first gap to be fully evaluated.
         pairs.sort(key=lambda pair: pair[1].index - pair[0].index, reverse=True)
         return pairs[0]
+
+    @staticmethod
+    def create_from_bgb_sequence(bgb_sequence: BiggestGapBisectionSequence) -> BiggestGapBisectionSearch:
+        """
+        Returns a BGB search object, which continues on state of the given BGB sequence object.
+
+        :param bgb_sequence: The BGB sequence object from which the state will be used to create the BGB search object.
+        """
+        return BiggestGapBisectionSearch(bgb_sequence._state_factory, completed_states=bgb_sequence._completed_states)
diff --git a/bci/search_strategy/bgb_sequence.py b/bci/search_strategy/bgb_sequence.py
index 92a9b77f..f59efde7 100644
--- a/bci/search_strategy/bgb_sequence.py
+++ b/bci/search_strategy/bgb_sequence.py
@@ -13,14 +13,15 @@ class BiggestGapBisectionSequence(SequenceStrategy):
     This sequence strategy will split the biggest gap between two states in half and return the state in the middle.
     """
 
-    def __init__(self, state_factory: StateFactory, limit: int) -> None:
+    def __init__(self, state_factory: StateFactory, limit: int, completed_states: Optional[list[State]]=None) -> None:
         """
         Initializes the sequence strategy.
 
         :param state_factory: The factory to create new states.
         :param limit: The maximum number of states to evaluate. 0 means no limit.
+        :param completed_states: States that have already been returned.
         """
-        super().__init__(state_factory, limit)
+        super().__init__(state_factory, limit, completed_states=completed_states)
         self._unavailability_gap_pairs: set[tuple[State, State]] = set()
         """Tuples in this list are **strict** boundaries of ranges without any available binaries."""
 
diff --git a/bci/search_strategy/composite_search.py b/bci/search_strategy/composite_search.py
index f59a7c10..90625e63 100644
--- a/bci/search_strategy/composite_search.py
+++ b/bci/search_strategy/composite_search.py
@@ -8,16 +8,19 @@
 class CompositeSearch():
     def __init__(self, state_factory: StateFactory, sequence_limit: int) -> None:
         self.sequence_strategy = BiggestGapBisectionSequence(state_factory, limit=sequence_limit)
-        self.search_strategy = BiggestGapBisectionSearch(state_factory)
-        self.sequence_strategy_finished = False
+        self.search_strategy = None
 
     def next(self) -> State:
-        # First we use the sequence strategy to select the next state
-        if not self.sequence_strategy_finished:
+        """
+        Returns the next state, based on a sequence strategy and search strategy.
+        First, the sequence strategy decides which state to return until it returns the SequenceFinished exception.
+        From then on, the search strategy decides which state to return.
+        """
+        if self.search_strategy is None:
             try:
                 return self.sequence_strategy.next()
             except SequenceFinished:
-                self.sequence_strategy_finished = True
+                self.search_strategy = BiggestGapBisectionSearch.create_from_bgb_sequence(self.sequence_strategy)
                 return self.search_strategy.next()
         else:
             return self.search_strategy.next()
diff --git a/bci/search_strategy/sequence_strategy.py b/bci/search_strategy/sequence_strategy.py
index 3a6eaff4..c93585fa 100644
--- a/bci/search_strategy/sequence_strategy.py
+++ b/bci/search_strategy/sequence_strategy.py
@@ -10,17 +10,18 @@
 
 
 class SequenceStrategy:
-    def __init__(self, state_factory: StateFactory, limit) -> None:
+    def __init__(self, state_factory: StateFactory, limit: int, completed_states: Optional[list[State]]=None) -> None:
         """
         Initializes the sequence strategy.
 
         :param state_factory: The factory to create new states.
         :param limit: The maximum number of states to evaluate. 0 means no limit.
+        :param completed_states: States that have already been returned.
         """
         self._state_factory = state_factory
         self._limit = limit
         self._lower_state, self._upper_state = self.__create_available_boundary_states()
-        self._completed_states = []
+        self._completed_states = completed_states if completed_states else []
 
     @abstractmethod
     def next(self) -> State:

From 0ebaf3ce44315ccfa46627b8094cd6ff2a410296 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Thu, 28 Nov 2024 09:05:44 +0000
Subject: [PATCH 53/57] Update BokehJS

---
 bci/web/vue/index.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bci/web/vue/index.html b/bci/web/vue/index.html
index a427ba2d..6bf8ba4b 100644
--- a/bci/web/vue/index.html
+++ b/bci/web/vue/index.html
@@ -4,8 +4,8 @@
     <meta charset="UTF-8" />
     <link rel="icon" href="public/bughog.ico">
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <script src="https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js"></script>
-    <script src="https://cdn.bokeh.org/bokeh/release/bokeh-api-3.4.1.min.js"></script>
+    <script src="https://cdn.bokeh.org/bokeh/release/bokeh-3.6.1.min.js"></script>
+    <script src="https://cdn.bokeh.org/bokeh/release/bokeh-api-3.6.1.min.js"></script>
     <title>BugHog</title>
   </head>
   <body class="bg-white text-[#213547] dark:bg-dark-1 dark:text-white">

From c5e563e2448b49195184a305b261cd257516df5f Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Thu, 28 Nov 2024 09:13:19 +0000
Subject: [PATCH 54/57] Upgrade python dependencies

---
 requirements.txt     | 14 ++++++----
 requirements_dev.txt | 66 ++++++++++++++++++++++++++++++++++++--------
 2 files changed, 63 insertions(+), 17 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 2a367b96..10050f30 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,10 @@
 #
-# This file is autogenerated by pip-compile with Python 3.12
+# This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
 #    pip-compile requirements.in
 #
-blinker==1.8.2
+blinker==1.9.0
     # via flask
 certifi==2024.8.30
     # via requests
@@ -16,7 +16,7 @@ dnspython==2.7.0
     # via pymongo
 docker==7.1.0
     # via -r requirements.in
-flask==3.0.3
+flask==3.1.0
     # via
     #   -r requirements.in
     #   flask-sock
@@ -40,10 +40,12 @@ markupsafe==3.0.2
     #   werkzeug
 mouseinfo==0.1.3
     # via pyautogui
-packaging==24.1
+packaging==24.2
     # via gunicorn
 pillow==11.0.0
-    # via -r requirements.in
+    # via
+    #   -r requirements.in
+    #   pyscreeze
 pyautogui==0.9.54
     # via -r requirements.in
 pygetwindow==0.0.9
@@ -80,7 +82,7 @@ urllib3==2.2.3
     # via
     #   docker
     #   requests
-werkzeug==3.0.4
+werkzeug==3.1.3
     # via flask
 wsproto==1.2.0
     # via simple-websocket
diff --git a/requirements_dev.txt b/requirements_dev.txt
index c9143ac6..3ef374bc 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -10,13 +10,13 @@ astroid==3.3.5
     # via pylint
 autopep8==2.3.1
     # via -r requirements_dev.in
-blinker==1.8.2
+blinker==1.9.0
     # via
     #   -r requirements.txt
     #   flask
-boto3==1.35.45
+boto3==1.35.71
     # via -r requirements_dev.in
-botocore==1.35.45
+botocore==1.35.71
     # via
     #   -r requirements_dev.in
     #   boto3
@@ -33,11 +33,11 @@ click==8.1.7
     # via
     #   -r requirements.txt
     #   flask
-coverage[toml]==7.6.4
+coverage[toml]==7.6.8
     # via
     #   -r requirements_dev.in
     #   pytest-cov
-debugpy==1.8.7
+debugpy==1.8.9
     # via -r requirements_dev.in
 dill==0.3.9
     # via pylint
@@ -51,7 +51,7 @@ flake8==7.1.1
     # via
     #   -r requirements_dev.in
     #   pytest-flake8
-flask==3.0.3
+flask==3.1.0
     # via
     #   -r requirements.txt
     #   flask-sock
@@ -96,42 +96,83 @@ mccabe==0.7.0
     # via
     #   flake8
     #   pylint
-packaging==24.1
+mouseinfo==0.1.3
+    # via
+    #   -r requirements.txt
+    #   pyautogui
+packaging==24.2
     # via
     #   -r requirements.txt
     #   anybadge
     #   gunicorn
     #   pytest
+pillow==11.0.0
+    # via
+    #   -r requirements.txt
+    #   pyscreeze
 platformdirs==4.3.6
     # via pylint
 pluggy==1.5.0
     # via pytest
+pyautogui==0.9.54
+    # via -r requirements.txt
 pycodestyle==2.12.1
     # via
     #   autopep8
     #   flake8
 pyflakes==3.2.0
     # via flake8
+pygetwindow==0.0.9
+    # via
+    #   -r requirements.txt
+    #   pyautogui
 pylint==3.3.1
     # via -r requirements_dev.in
 pymongo==4.10.1
     # via -r requirements.txt
+pymsgbox==1.0.9
+    # via
+    #   -r requirements.txt
+    #   pyautogui
+pyperclip==1.9.0
+    # via
+    #   -r requirements.txt
+    #   mouseinfo
+pyrect==0.2.0
+    # via
+    #   -r requirements.txt
+    #   pygetwindow
+pyscreeze==1.0.1
+    # via
+    #   -r requirements.txt
+    #   pyautogui
 pytest==8.3.3
     # via
     #   -r requirements_dev.in
     #   pytest-cov
     #   pytest-flake8
-pytest-cov==5.0.0
+pytest-cov==6.0.0
     # via -r requirements_dev.in
-pytest-flake8==1.2.1
+pytest-flake8==1.3.0
     # via -r requirements_dev.in
 python-dateutil==2.9.0.post0
     # via botocore
+python3-xlib==0.15
+    # via
+    #   -r requirements.txt
+    #   mouseinfo
+    #   pyautogui
+pytweening==1.2.0
+    # via
+    #   -r requirements.txt
+    #   pyautogui
+pyvirtualdisplay==3.0
+    # via -r requirements.txt
 requests==2.32.3
     # via
     #   -r requirements.txt
     #   docker
-s3transfer==0.10.3
+s3transfer==0.10.4
     # via boto3
 simple-websocket==1.1.0
     # via
@@ -142,6 +183,7 @@ six==1.16.0
     #   -r requirements.txt
     #   flatten-dict
     #   python-dateutil
+    #   xlib
 tomlkit==0.13.2
     # via pylint
 urllib3==2.2.3
@@ -150,7 +192,7 @@ urllib3==2.2.3
     #   botocore
     #   docker
     #   requests
-werkzeug==3.0.4
+werkzeug==3.1.3
     # via
     #   -r requirements.txt
     #   flask
@@ -158,3 +200,5 @@ wsproto==1.2.0
     # via
     #   -r requirements.txt
     #   simple-websocket
+xlib==0.21
+    # via -r requirements.txt

From 4a9a5a5e2c9b864cf3249c8a2642c2728767d33e Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Thu, 28 Nov 2024 09:42:12 +0000
Subject: [PATCH 55/57] Add convenience scripts for updating pip and npm
 dependencies

---
 scripts/node_update.sh | 3 +++
 scripts/pip_update.sh  | 4 ++++
 2 files changed, 7 insertions(+)
 create mode 100755 scripts/node_update.sh
 create mode 100755 scripts/pip_update.sh

diff --git a/scripts/node_update.sh b/scripts/node_update.sh
new file mode 100755
index 00000000..24cd6576
--- /dev/null
+++ b/scripts/node_update.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+exec docker run -v ${PWD}/bci/web/vue/:/app -w /app node:lts-alpine npm update
diff --git a/scripts/pip_update.sh b/scripts/pip_update.sh
new file mode 100755
index 00000000..150c577f
--- /dev/null
+++ b/scripts/pip_update.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+pip-compile -U requirements.in
+pip-compile -U requirements_dev.in

From 2d19a14345215141f900a9c5ac7ab380ac628a05 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Thu, 28 Nov 2024 09:43:42 +0000
Subject: [PATCH 56/57] Update node dependencies

---
 bci/web/vue/package-lock.json | 450 ++++++++++++++++++++++++----------
 1 file changed, 317 insertions(+), 133 deletions(-)

diff --git a/bci/web/vue/package-lock.json b/bci/web/vue/package-lock.json
index 1a1d035c..e393c6a9 100644
--- a/bci/web/vue/package-lock.json
+++ b/bci/web/vue/package-lock.json
@@ -29,6 +29,7 @@
       "resolved": "https://registry.npmjs.org/@alloc/quick-lru/-/quick-lru-5.2.0.tgz",
       "integrity": "sha512-UrcABB+4bUrFABwbluTIBErXwvbsU/V7TZWfmbgJfbkwiBuziS9gxdODUyuiecfdGQ85jglMW6juS3+z5TsKLw==",
       "dev": true,
+      "license": "MIT",
       "engines": {
         "node": ">=10"
       },
@@ -40,6 +41,7 @@
       "version": "7.25.9",
       "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.25.9.tgz",
       "integrity": "sha512-4A/SCr/2KLd5jrtOMFzaKjVtAei3+2r/NChoBNoZ3EyP/+GlhoaEGoWOZUmFmoITP7zOJyHIMm+DYRd8o3PvHA==",
+      "license": "MIT",
       "engines": {
         "node": ">=6.9.0"
       }
@@ -48,16 +50,18 @@
       "version": "7.25.9",
       "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.25.9.tgz",
       "integrity": "sha512-Ed61U6XJc3CVRfkERJWDz4dJwKe7iLmmJsbOGu9wSloNSFttHV0I8g6UAgb7qnK5ly5bGLPd4oXZlxCdANBOWQ==",
+      "license": "MIT",
       "engines": {
         "node": ">=6.9.0"
       }
     },
     "node_modules/@babel/parser": {
-      "version": "7.25.9",
-      "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.25.9.tgz",
-      "integrity": "sha512-aI3jjAAO1fh7vY/pBGsn1i9LDbRP43+asrRlkPuTXW5yHXtd1NgTEMudbBoDDxrf1daEEfPJqR+JBMakzrR4Dg==",
+      "version": "7.26.2",
+      "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.26.2.tgz",
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       "version": "4.2.3",
       "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
       "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
         "emoji-regex": "^8.0.0",
         "is-fullwidth-code-point": "^3.0.0",
@@ -2368,6 +2550,7 @@
       "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
       "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
         "ansi-regex": "^5.0.1"
       },
@@ -2376,10 +2559,11 @@
       }
     },
     "node_modules/yaml": {
-      "version": "2.6.0",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.6.0.tgz",
-      "integrity": "sha512-a6ae//JvKDEra2kdi1qzCyrJW/WZCgFi8ydDV+eXExl95t+5R+ijnqHJbz9tmMh8FUjx3iv2fCQ4dclAQlO2UQ==",
+      "version": "2.6.1",
+      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.6.1.tgz",
+      "integrity": "sha512-7r0XPzioN/Q9kXBro/XPnA6kznR73DHq+GXh5ON7ZozRO6aMjbmiBuKste2wslTFkC5d1dw0GooOCepZXJ2SAg==",
       "dev": true,
+      "license": "ISC",
       "bin": {
         "yaml": "bin.mjs"
       },

From 8dcb3f079118f6a12ccc686fbd65e436234f2e25 Mon Sep 17 00:00:00 2001
From: Gertjan <gertjan.franken@kuleuven.be>
Date: Thu, 28 Nov 2024 10:51:41 +0000
Subject: [PATCH 57/57] Fix test failing due to changed internals

---
 test/sequence/test_composite_search.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/test/sequence/test_composite_search.py b/test/sequence/test_composite_search.py
index 5a7d247a..8728c8f3 100644
--- a/test/sequence/test_composite_search.py
+++ b/test/sequence/test_composite_search.py
@@ -23,7 +23,6 @@ def test_binary_sequence_always_available_composite(self):
             outcome_func=lambda x: True if x < 50 else False,
             evaluated_indexes=[0, 99, 49, 74, 24, 36, 61, 86, 12, 42]
         )
-        sequence.search_strategy._state_factory = state_factory
 
         # Sequence
         index_sequence = [sequence.next().index for _ in range(3)]
@@ -47,7 +46,6 @@ def test_binary_sequence_always_available_composite_two_shifts(self):
             outcome_func=lambda x: True if x < 33 or 81 < x else False,
             evaluated_indexes=[0, 99, 49, 74, 24, 36, 61, 86, 12, 42]
         )
-        sequence.search_strategy._state_factory = state_factory
 
         while True:
             try:
@@ -57,7 +55,7 @@ def test_binary_sequence_always_available_composite_two_shifts(self):
 
         evaluated_indexes = [state.index for state in sequence.search_strategy._completed_states]
 
-        assert sequence.sequence_strategy_finished
+        assert sequence.search_strategy is not None
         assert 32 in evaluated_indexes
         assert 33 in evaluated_indexes
         assert 81 in evaluated_indexes