Adding Settings Menu

.gitignore

@@ -3,6 +3,9 @@
 user_data/runs/*
 user_data/workflows/*
 user_data/external_data/*
+user_data/settings/*
+!user_data/settings/plots_default.yaml
+!user_data/settings/databases_default.yaml
 user_data/debug/*
 ui/static/admin/*
 ui/uploads/*

protzilla/constants/paths.py

@@ -4,6 +4,7 @@
 USER_DATA_PATH = Path(PROJECT_PATH, "user_data")
 RUNS_PATH = USER_DATA_PATH / "runs"
 WORKFLOWS_PATH = USER_DATA_PATH / "workflows"
+SETTINGS_PATH = USER_DATA_PATH / "settings"
 EXTERNAL_DATA_PATH = Path(PROJECT_PATH, "user_data/external_data")
 WORKFLOW_META_PATH = Path(PROJECT_PATH, "protzilla/constants/workflow_meta.json")
 UI_PATH = Path(PROJECT_PATH, "ui")

protzilla/data_preprocessing/plots.py

@@ -7,7 +7,6 @@
 
 from protzilla.data_preprocessing.plots_helper import generate_tics
 from protzilla.utilities import default_intensity_column
-from protzilla.utilities.plot_template import *
 from protzilla.constants.colors import *
 
 def create_pie_plot(

protzilla/steps.py

@@ -9,7 +9,8 @@
 from pathlib import Path
 
 import pandas as pd
-import plotly
+import plotly.io as pio
+import plotly.graph_objects as go
 from PIL import Image
 
 from protzilla.utilities import format_trace
@@ -277,33 +278,47 @@ def __repr__(self):
     def empty(self) -> bool:
         return len(self.plots) == 0
 
-    def export(self, format_):
+    def export(self, settings: dict) -> list:
+        """
+        Converts all plots from this step to files according to the format and size in the Plotly template.
+        An exported plot is represented as BytesIO object containing binary image data.
+        :param settings: Dict containing the plot settings.
+        :return: List of all exported plots.
+        """
+        from ui.settings.plot_template import get_scale_factor
         exports = []
+        format_ = settings["file_format"]
+
         for plot in self.plots:
-            if isinstance(plot, plotly.graph_objs.Figure):
-                if format_ in ["eps", "tiff"]:
-                    png_binary = plotly.io.to_image(plot, format="png", scale=4)
-                    img = Image.open(BytesIO(png_binary)).convert("RGB")
+            scale_factor = get_scale_factor(plot, settings)
+            # For Plotly GO Figure
+            if isinstance(plot, go.Figure):
+                if format_ in ["tiff", "eps"]:
+                    binary_png = pio.to_image(plot, format="png", scale=scale_factor)
+                    img = Image.open(BytesIO(binary_png)).convert("RGB")
                     binary = BytesIO()
                     if format_ == "tiff":
                         img.save(binary, format="tiff", compression="tiff_lzw")
-                    else:
+                    elif format_ == "eps":
                         img.save(binary, format=format_)
+                    binary.seek(0)
                     exports.append(binary)
                 else:
-                    binary_string = plotly.io.to_image(plot, format=format_, scale=4)
-                    exports.append(BytesIO(binary_string))
+                    binary_png = pio.to_image(plot, format=format_, scale=scale_factor)
+                    exports.append(BytesIO(binary_png))
             elif isinstance(plot, dict) and "plot_base64" in plot:
                 plot = plot["plot_base64"]
 
-            if isinstance(plot, bytes):  # base64 encoded plots
-                if format_ in ["eps", "tiff"]:
+            # TO DO: Include scale_factor here
+            # For base64 encoded plot
+            if isinstance(plot, bytes):
+                if format_ in ["tiff", "eps"]:
                     img = Image.open(BytesIO(base64.b64decode(plot))).convert("RGB")
                     binary = BytesIO()
                     if format_ == "tiff":
                         img.save(binary, format="tiff", compression="tiff_lzw")
-                    else:
-                        img.save(binary, format=format_)
+                    elif format_ == "eps":
+                        img.save(binary, format="eps")
                     binary.seek(0)
                     exports.append(binary)
                 elif format_ in ["png", "jpg"]:

protzilla/utilities/utilities.py

@@ -11,6 +11,7 @@
 import pandas as pd
 import psutil
 
+from django.http import QueryDict
 
 # recipie from https://docs.python.org/3/library/itertools.html
 def unique_justseen(iterable, key=None):
@@ -136,3 +137,47 @@ def get_file_name_from_upload_path(upload_path: str) -> str:
     base_name = file_name_randomized.split("_")[0]
     file_extension = file_name_randomized.split(".")[-1]
     return f"{base_name}.{file_extension}"
+
+
+def parameters_from_post(post: QueryDict) -> dict:
+    """
+    Removes token from dict and converts the remaining entries into suitable data formats.
+    :param post: Django dict containing POST data.
+    :return: Dict containing the parameters in suitable formats.
+    """
+    d = dict(post)
+    if "csrfmiddlewaretoken" in d:
+        del d["csrfmiddlewaretoken"]
+    parameters = {}
+    for k, v in d.items():
+        if len(v) > 1:
+            # only used for named_output parameters and multiselect fields
+            parameters[k] = v
+        else:
+            parameters[k] = convert_str_if_possible(v[0])
+    return parameters
+
+
+def convert_str_if_possible(s):
+    """
+    Converts an input value into suitable representation as a string.
+    :param s: Input value.
+    :return: Converted input value.
+    """
+    try:
+        f = float(s)
+        return int(f) if int(f) == f else f
+    except ValueError:
+        if s == "checked":
+            # s is a checkbox
+            return True
+        if re.fullmatch(r"\d+(\.\d+)?(\|\d+(\.\d+)?)*", s):
+            # s is a multi-numeric input e.g. 1-0.12-5
+            numbers_str = re.findall(r"\d+(?:\.\d+)?", s)
+            numbers = []
+            for num in numbers_str:
+                num = float(num)
+                num = int(num) if int(num) == num else num
+                numbers.append(num)
+            return numbers
+        return s

tests/ui/test_settings.py

@@ -0,0 +1,41 @@
+import pytest
+import plotly.graph_objects as go
+
+from protzilla.constants.colors import PLOT_PRIMARY_COLOR, PLOT_SECONDARY_COLOR
+from protzilla.constants.paths import SETTINGS_PATH
+from ui.settings.plot_template import (
+    determine_font,
+    resize_for_display,
+    get_scale_factor
+)
+
+
+@pytest.fixture
+def sample_params():
+    return {
+        "section_id": "plots",
+        "file_format": "png",
+        "width": 85,
+        "height": 60,
+        "custom_font": "Ubuntu Mono",
+        "font": "Arial",
+        "heading_size": 11,
+        "text_size": 8
+    }
+
+def test_determine_font(sample_params):
+    assert determine_font(sample_params) == "Arial"
+    sample_params["font"] = "Custom"
+    assert determine_font(sample_params) == "Ubuntu Mono"
+
+def test_resize_for_display(sample_params):
+    result = resize_for_display(sample_params)
+    assert result["display_width"] == 600  # SCALED_WIDTH
+    assert result["display_heading_size"] == 27
+
+def test_get_scale_factor(sample_params):
+    fig = go.Figure()
+    fig.update_layout(width=600)
+    scale = get_scale_factor(fig, sample_params)
+    assert isinstance(scale, float)
+    assert round(scale, 3) == 1.673

ui/main/settings.py

@@ -47,6 +47,7 @@
     "django.contrib.messages",
     "django.contrib.staticfiles",
     "runs",
+    "settings",
 ]
 
 MIDDLEWARE = [
@@ -127,7 +128,10 @@
 
 STATIC_URL = "static/"
 
-STATICFILES_DIRS = [BASE_DIR / "static"]
+STATICFILES_DIRS = [
+    BASE_DIR / "static",
+    BASE_DIR / "settings/static"
+    ]
 
 # Default primary key field type
 # https://docs.djangoproject.com/en/4.1/ref/settings/#default-auto-field

ui/main/urls.py

@@ -21,6 +21,7 @@
 urlpatterns = [
     path("", views.index),
     path("runs/", include("runs.urls")),
+    path("settings/", include("settings.urls")),
     path("databases", views.databases, name="databases"),
     path("databases/upload", views.database_upload, name="database_upload"),
     path("databases/delete", views.database_delete, name="database_delete"),

ui/main/views.py

@@ -19,6 +19,7 @@ def index(request):
 
 
 def databases(request):
+    request.session['last_view'] = "databases"
     databases = uniprot_databases()
     df_infos = {}
     if database_metadata_path.exists():

ui/runs/static/runs/style.css

@@ -88,4 +88,10 @@ html, body {
     padding: 10px 8%;
     margin-top: 10px;
     background-color: rgb(255, 255, 255);
+}
+.plot-wrapper {
+    width: fit-content;
+    height: fit-content;
+    border: 1px solid #e8edf3;
+    border-radius: .375rem;
 }

ui/runs/templates/runs/details.html

@@ -215,7 +215,7 @@ <h3>{{ display_name }}</h3>
                 {% if current_plots %}
                     <div class="mt-4" id="plots">
                         {% for plot in current_plots %}
-                            <div class="plot-wrapper">
+                            <div class="plot-wrapper mb-2">
                                 {{ plot|safe }}
                             </div>
                         {% endfor %}
@@ -225,15 +225,13 @@ <h3>{{ display_name }}</h3>
                     <div class="d-flex col">
                         {% if current_plots %}
                             <form action="{% url 'runs:download_plots' run_name %}">
-                                <select class="form-select mb-2" name="format">
-                                    <option value="png" selected="selected">png</option>
-                                    <option value="tiff">tiff</option>
-                                    <option value="svg">svg</option>
-                                    <option value="pdf">pdf</option>
-                                    <option value="eps">eps</option>
-                                    <option value="jpg">jpg</option>
-                                </select>
-                                <button class="btn btn-grey">Download plots</button>
+                                <button class="btn btn-grey d-flex align-items-center">
+                                    <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-download me-2" viewBox="0 0 16 16">
+                                        <path d="M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5"/>
+                                        <path d="M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708z"/>
+                                    </svg>
+                                    Download plots
+                                </button>
                             </form>
                         {% endif %}
                     </div>
@@ -278,11 +276,11 @@ <h5 class="modal-title" id="calculationInProgressModalLabel">Do you want back?</
                                                             Do you want to proceed?
                                                             <hr>
                                                             <a href="{% url 'runs:back' run_name %}" id = "backButton" class="btn btn-red mr-auto">Back</a>
-                                                            <button id= "cancel" type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
+                                                            <button id="cancel" type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
+                                                        </div>
                                                     </div>
                                                 </div>
                                             </div>
-                                        </div>
                                         {% endif %}
                                         {% if not last_step %}
                                           <button class="btn btn-red" {% if not results_exist %} disabled {% endif %} >Next</button>

ui/runs/views.py

@@ -29,6 +29,7 @@
     format_trace,
     get_memory_usage,
     name_to_title,
+    parameters_from_post,
 )
 from protzilla.workflow import get_available_workflow_names
 from protzilla.constants.paths import WORKFLOWS_PATH
@@ -38,13 +39,14 @@
     make_name_field,
     make_sidebar,
 )
-from ui.runs.views_helper import display_message, display_messages, parameters_from_post
+from ui.runs.views_helper import display_message, display_messages
 
 from .form_mapping import (
     get_empty_plot_form_by_method,
     get_filled_form_by_method,
     get_filled_form_by_request,
 )
+from ui.settings.views import load_settings
 
 active_runs: dict[str, Run] = {}
 
@@ -68,6 +70,9 @@ def detail(request: HttpRequest, run_name: str):
         active_runs[run_name] = Run(run_name)
     run: Run = active_runs[run_name]
 
+    request.session['last_view'] = "runs:detail"
+    request.session['run_name'] = run_name
+
     # section, step, method = run.current_run_location()
     # end_of_run = not step
 
@@ -173,6 +178,9 @@ def index(request: HttpRequest, index_error: bool = False):
     :return: the rendered index page
     :rtype: HttpResponse
     """
+
+    request.session['last_view'] = "runs:index"
+
     return render(
         request,
         "runs/index.html",
@@ -447,11 +455,14 @@ def download_plots(request: HttpRequest, run_name: str):
     if run_name not in active_runs:
         active_runs[run_name] = Run(run_name)
     run = active_runs[run_name]
-    format_ = request.GET["format"]
+    settings = load_settings("plots")
+    format_ = settings["file_format"]
     index = run.steps.current_step_index
     section = run.current_step.section
     operation = run.current_step.operation
-    exported = run.current_plots.export(format_=format_)
+    exported = run.current_plots.export(settings)
+    if len(exported) == 0:
+        raise RuntimeError("List of exported plots is empty.")
     if len(exported) == 1:
         filename = f"{index}-{section}-{operation}.{format_}"
         return FileResponse(exported[0], filename=filename, as_attachment=True)