Merge pull request #142 from bptlab/refactor/133-tracex-pj-generator

Refactor/133 tracex pj generator
bptlab · May 26, 2024 · 62e9d79 · 62e9d79
2 parents 0dee86c + 3643fc6
commit 62e9d79
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Showing 42 changed files with 711 additions and 502 deletions.
diff --git a/tracex_project/db.sqlite3 b/tracex_project/db.sqlite3
diff --git a/tracex_project/db_results/templates/db_results_overview.html b/tracex_project/db_results/templates/db_results_overview.html
@@ -3,7 +3,7 @@
 <head>
     <title>Database Results</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
 </head>
 <body class="main_body">
 <img src="{% static '/tracex/img/database_results_logo.png' %}" alt="Database Results Logo"
@@ -23,7 +23,7 @@ <h2>Welcome to the Database Results</h2>
 </div>
 
 <a href="{% url 'landing_page' %}">
-    <button class="menu_button">Return to TracEX menu</button>
+    <button class="menu_button">Return to TracEX Menu</button>
 </a>
 </body>
 </html>
diff --git a/tracex_project/db_results/templates/evaluation.html b/tracex_project/db_results/templates/evaluation.html
@@ -6,7 +6,7 @@
     <title>Evaluation View</title>
     {% load static %}
     <link href="https://cdn.jsdelivr.net/npm/[email protected]/distribute/nouislider.min.css" rel="stylesheet">
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
     <script src="https://cdn.jsdelivr.net/npm/[email protected]/distribute/nouislider.min.js"></script>
     <script src="https://code.jquery.com/jquery-3.6.4.min.js"></script>
     <script src="{% static '/db_results/js/filter_toggle.js' %}" defer></script>
@@ -17,7 +17,7 @@ <h1 style="text-align: center">Evaluation View</h1>
 
 <!-- Display complete event log -->
 <div>
-    <button id="toggleButton1">Show/Hide Event Log with applied filters</button>
+    <button id="toggleButton1" class="function_button">Show/Hide Event Log with applied filters</button>
     <div id="contentWrapper1" style="display: none;">
         {% if event_log_table %}
             <p></p>
@@ -31,7 +31,7 @@ <h1 style="text-align: center">Evaluation View</h1>
 </div>
 
 <div>
-    <button id="toggleButton2" style="margin-top: 1em">Show/Hide Cohorts belonging to remaining entries</button>
+    <button id="toggleButton2" class="function_button" style="margin-top: 1em">Show/Hide Cohorts belonging to remaining entries</button>
     <div id="contentWrapper2" style="display: none;">
         {% if cohorts_table %}
             <p></p>
@@ -143,12 +143,11 @@ <h1 style="text-align: center">Evaluation View</h1>
 
     {{ form.errors }}
 
-    <input type="submit" value="Refresh Filter" class="button">
+    <input type="submit" value="Refresh Filter" class="function_button">
 </form>
-<br>
 
 <!-- Trigger/Open The Modal (XES Download) -->
-<button id="downloadBtn" class="button">Download XES File</button>
+<button id="downloadBtn" class="function_button">Download XES File</button>
 <div id="downloadModal" class="modal">
     <div class="modal-content">
         <span class="close">&times;</span>

diff --git a/tracex_project/db_results/templates/metrics_dashboard.html b/tracex_project/db_results/templates/metrics_dashboard.html
@@ -3,7 +3,7 @@
 <head>
     <title>Metrics Dashboard</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
     <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
     <script src="{% static '/db_results/js/metrics-dashboard.js' %}" defer></script>
 </head>
@@ -117,7 +117,7 @@ <h3>Timestamp Correctnes Bar Chart</h3>
     <button class="menu_button">Return to Database Results Overview</button>
 </a>
 <a href="{% url 'landing_page' %}">
-    <button class="menu_button">Return to TracEX menu</button>
+    <button class="menu_button">Return to TracEX Menu</button>
 </a>
 </body>
 </html>
diff --git a/tracex_project/db_results/templates/metrics_pj_overview.html b/tracex_project/db_results/templates/metrics_pj_overview.html
@@ -3,7 +3,7 @@
 <head>
     <title>Metrics Overview</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
 </head>
 <body class="main_body">
 <img src="{% static '/tracex/img/result_dashboard_logo.png' %}" alt="Metrics Dashboard" class="metrics_dashboard_logo">
@@ -15,15 +15,15 @@ <h2>Welcome to the Metrics Dashboard</h2>
 <form method="post">
     {% csrf_token %}
     {{ form.as_p }}
-    <button type="submit" class="menu_button">Select this Patient Journey</button>
+    <button type="submit" class="function_button">Select this Patient Journey</button>
 </form>
 
 <a href="{% url 'db_results_overview' %}">
     <button class="menu_button">Return to Database Results Overview</button>
 </a>
 
 <a href="{% url 'landing_page' %}">
-    <button class="menu_button">Return to TracEX menu</button>
+    <button class="menu_button">Return to TracEX Menu</button>
 </a>
 </body>
 </html>
diff --git a/tracex_project/extraction/logic/modules/module_metrics_analyzer.py b/tracex_project/extraction/logic/modules/module_metrics_analyzer.py
@@ -105,9 +105,8 @@ def __rate_timestamps_correctness(
             }
         )
 
-        timestamp_correctness, top_logprops = u.query_gpt(
-            messages, logprobs=True, top_logprobs=1
+        timestamp_correctness, linear_probability = u.query_gpt(
+            messages, return_linear_probability=True, top_logprobs=1
         )
-        linear_prop = u.calculate_linear_probability(top_logprops[0].logprob)
 
-        return timestamp_correctness, linear_prop
+        return timestamp_correctness, linear_probability
diff --git a/tracex_project/extraction/logic/orchestrator.py b/tracex_project/extraction/logic/orchestrator.py
@@ -162,7 +162,7 @@ def initialize_modules(self):
         }
         return modules
 
-    def run(self, view=None) -> pd.DataFrame:
+    def run(self, view=None) -> None:
         """Run the modules and set default values for modules not executed."""
         modules = self.initialize_modules()
         execution_step: int = 1
@@ -257,7 +257,7 @@ def set_default_values(self) -> None:
         data = self.get_data()
 
         if "time_extraction" not in config_modules:
-            DataFrameUtilities.set_default_timestamps(data)
+            data = DataFrameUtilities.set_default_timestamps(data)
         if "event_type_classification" not in config_modules:
             data["event_type"] = "N/A"
         if "location_extraction" not in config_modules:

diff --git a/tracex_project/extraction/templates/choose_input_method.html b/tracex_project/extraction/templates/choose_input_method.html
@@ -4,7 +4,7 @@
     <meta charset="UTF-8">
     <title>Choose Input Method</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static 'tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
 </head>
 <body class="main_body">
     <header>
@@ -16,19 +16,19 @@ <h2>Choose Input Method</h2>
         <section class="form-row">
             <div class="form-column">
                 <a href='{% url "journey_upload" %}'>
-                    <button class="menu_button">Upload a patient journey</button>
+                    <button class="menu_button">Upload a Patient Journey</button>
                 </a>
             </div>
             <div class="form-column">
                 <a href='{% url "journey_select" %}'>
-                    <button class="menu_button">Select a patient journey</button>
+                    <button class="menu_button">Select a Patient Journey</button>
                 </a>
             </div>
         </section>
     </main>
     <footer>
         <a href="{% url 'landing_page' %}">
-            <button class="menu_button">Return to TracEX menu</button>
+            <button class="menu_button">Return to TracEX Menu</button>
         </a>
     </footer>
 </body>

diff --git a/tracex_project/extraction/templates/filter_journey.html b/tracex_project/extraction/templates/filter_journey.html
@@ -3,7 +3,7 @@
     <title>Upload Journey</title>
     {% load static %}
     <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/loading-spinner.css' %}">
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
     <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/progress-bar.css' %}">
     <script src="{% static '/tracex/js/progress-bar.js' %}" defer></script>
     <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.7.1/jquery.min.js"></script>
@@ -322,7 +322,7 @@ <h4>DFG activity key</h4>
         <div class="progress-container">
         </div>
     </div>
-    <input type="submit" value="Execute Extraction Pipeline" id="progress_button" class="button"
+    <input type="submit" value="Execute Extraction Pipeline" id="progress_button" class="function_button"
            onclick="disableButton()">
     <script>
         function disableButton() {
@@ -335,6 +335,6 @@ <h4>DFG activity key</h4>
     <button class="menu_button">Previous</button>
 </a>
 <a href="{% url "landing_page" %}">
-    <button class="menu_button">Return to TracEX menu</button>
+    <button class="menu_button">Return to TracEX Menu</button>
 </a>
 </body>
diff --git a/tracex_project/extraction/templates/journey_details.html b/tracex_project/extraction/templates/journey_details.html
@@ -4,7 +4,7 @@
     <meta charset="UTF-8">
     <title>Select Journey</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
 </head>
 
 <body class="main_body">
@@ -14,13 +14,13 @@ <h2>Content of "{{ patient_journey.name }}"</h2>
 
     <form method="post" action="{% url 'journey_details' pk=patient_journey.pk %}">
         {% csrf_token %}
-        <input type="submit" value="Next" class="button">
+        <input type="submit" class="function_button" value="Confirm Selection">
     </form>
     <a href="{% url "journey_select" %}">
         <button class="menu_button">Previous</button>
     </a>
     <a href="{% url "landing_page" %}">
-        <button class="menu_button">Return to TracEX menu</button>
+        <button class="menu_button">Return to TracEX Menu</button>
     </a>
 </body>
 </html>
diff --git a/tracex_project/extraction/templates/result.html b/tracex_project/extraction/templates/result.html
@@ -5,7 +5,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
     <title>Result</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
     <script src="{% static '/tracex/js/pop_up_xes.js' %}" defer></script>
 </head>
 <body class="main_body">
@@ -28,7 +28,7 @@ <h1>Success! The TracEX pipeline produced the following results:</h1>
     </script>
 
     {% if trace_table %}
-        <button id="toggleButton1">Show/Hide extracted Event Log from Journey</button>
+        <button id="toggleButton1" class="function_button">Show/Hide extracted Trace from Journey</button>
         <div id="contentWrapper1" style="display: none;">
             <p><b>This is the event log extracted from the journey above.</b></p>
             <div id="xesContent1" class="xes_container">{{ trace_table|safe }}</div>
@@ -38,7 +38,7 @@ <h1>Success! The TracEX pipeline produced the following results:</h1>
     {% endif %}
 
     {% if event_log_table %}
-        <button id="toggleButton2">Show/Hide enriched Event Log</button>
+        <button id="toggleButton2" class="function_button">Show/Hide enriched Event Log</button>
         <div id="contentWrapper2" style="display: none;">
             <p><b>This is the event log enriched by the extracted trace.</b></p>
             <div id="xesContent2" class="xes_container">{{ event_log_table|safe }}</div>
@@ -111,10 +111,11 @@ <h4>DFG Activity Key</h4>
                 {% endfor %}
             </div>
         {% endif %}
-        <input type="submit" value="Refresh Filter" class="button">
+        <input type="submit" value="Refresh Filter" class="function_button">
     </form>
 
-    <button id="downloadBtn" class="button">Download XES File</button>
+    <!-- Trigger/Open The Modal (XES Download) -->
+    <button id="downloadBtn" class="function_button">Download XES File</button>
     <div id="downloadModal" class="modal">
         <div class="modal-content">
             <span class="close">&times;</span>
@@ -130,10 +131,10 @@ <h4>DFG Activity Key</h4>
         </div>
     </div>
     <a href="{% url "save_success" %}">
-        <button class="menu_button">Save results to the database</button>
+        <button class="function_button">Save Results to the Database</button>
     </a>
     <a href="{% url "choose_input_method" %}">
-        <button class="menu_button">Return to input selection</button>
+        <button class="menu_button">Return to Input Selection</button>
     </a>
     <a href="{% url "landing_page" %}">
         <button class="menu_button">Return to TracEX Menu</button>

diff --git a/tracex_project/extraction/templates/save_success.html b/tracex_project/extraction/templates/save_success.html
@@ -5,15 +5,15 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
     <title>Result</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
 </head>
 <body class="main_body">
     <h1>Success! Results have been saved to the database.</h1>
     <a href="{% url "choose_input_method" %}">
-        <button class="menu_button">Return to input selection</button>
+        <button class="menu_button">Return to Input Selection</button>
     </a>
     <a href="{% url "landing_page" %}">
-        <button class="menu_button">Return to TracEX menu</button>
+        <button class="menu_button">Return to TracEX Menu</button>
     </a>
 </body>
 </html>
diff --git a/tracex_project/extraction/templates/select_journey.html b/tracex_project/extraction/templates/select_journey.html
@@ -4,7 +4,7 @@
     <meta charset="UTF-8">
     <title>Select Journey</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
 </head>
 
 <body class="main_body">
@@ -15,14 +15,14 @@ <h2>Select Patient Journey from Database</h2>
     <form method="post">
         {% csrf_token %}
         {{ form.as_p }}
-        <button type="submit" class="menu_button">Next</button>
+        <button type="submit" class="function_button">Select this Patient Journey</button>
     </form>
 
     <a href="{% url "choose_input_method" %}">
-        <button class="menu_button">Return to input method selection</button>
+        <button class="menu_button">Return to Input Method Selection</button>
     </a>
     <a href="{% url "landing_page" %}">
-        <button class="menu_button">Return to TracEX menu</button>
+        <button class="menu_button">Return to TracEX Menu</button>
     </a>
 </body>
 </html>
diff --git a/tracex_project/extraction/templates/upload_journey.html b/tracex_project/extraction/templates/upload_journey.html
@@ -2,7 +2,7 @@
 <head>
     <title>Upload Journey</title>
     {% load static %}
-    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/style.css' %}">
+    <link rel="stylesheet" type="text/css" href="{% static '/tracex/css/styles.css' %}">
 </head>
 
 
@@ -29,10 +29,10 @@ <h2>Upload Patient Journey</h2>
             </div>
         </div>
 
-        <input type="submit" value="Next" class="button">
+        <input type="submit" class="function_button" value="Upload this Patient Journey">
     </form>
     <a href="{% url "choose_input_method" %}">
-        <button class="menu_button">Return to input method selection</button>
+        <button class="menu_button">Return to Input Method Selection</button>
     </a>
     <a href="{% url "landing_page" %}">
         <button class="menu_button">Return to TracEX menu</button>

diff --git a/tracex_project/patient_journey_generator/forms.py b/tracex_project/patient_journey_generator/forms.py
@@ -4,11 +4,23 @@
 
 
 class GenerationOverviewForm(forms.ModelForm):
-    """Form for viewing generated patient journey."""
+    """
+    Form for generating a patient journey.
+
+    By submitting this form, a patient journey is generated and saved in the orchestrator's configuration.
+    """
 
     class Meta:
-        """Metaclass for GenerationForm, provides additional parameters for the form."""
+        """
+        Metaclass that provides additional information.
 
+        Attributes:
+        model -- The model to use for the form.
+        fields -- The fields to include in the form.
+        help_texts -- The help texts for the fields.
+        widgets -- The widgets for the fields.
+        - "name" - A text input field to name the patient journey. Required, to save patient journey in the database.
+        """
         model = PatientJourney
         fields = ["name"]
         help_texts = {