Adding Settings Menu (#552)

* added basic construct of settings page

* added selection of sections and forms for plot settings

* moved settings file to own folder, added navigation to sidebar and small enhancements

* Added footer and returning to last view after saving or canceling

* small bugfix and refactoring

* Fixed alignment

* enabled saving and loading settings, split settings into sections and moved some methods

* connected and enhanced plotly template, added small ui changes

* minor changes

* moved plot_template to settings folder

* restructured plot settings html, enabled choosing a custom font

* included file format from settings in plot download

* added plot height and width into plot template

* added plot settings preview

* moved js code from <script> into own js file

* moved plot preview in column, some formatting

* adjusted spacing, added convertion from mm to px

* fixed behaviour of unsaved changes modal

* added default yamls as fallback templates

* removed plot.yaml

* adjusted gitignore for ignoring individual settings

* small bugfix

* added check if list of exported plots is empty

* enhanced plot download by including scaling to experienced size, added some documentation

* fixed broken tiff & eps download with plotly figures

* removed general section, added temporary databases section

* added font scaling to displayed plots

* added requested changes

* added tests

* attempt to fix tests that were successful locally

* removed unused imports

* added requested changes

Author: ronjakrg

.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

@@ -10,7 +10,8 @@
 from typing import Literal
 
 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
@@ -284,33 +285,47 @@ 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/plot_template.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

protzilla/utilities/utilities.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

tests/ui/test_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/settings.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/urls.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():