Add requested examples

.github/workflows/test.yml

@@ -2,6 +2,10 @@ name: ci
 
 on: [push]
 
+env:
+  GALAXY_URL: "${{ secrets.GALAXY_URL }}"
+  GALAXY_API_KEY: "${{ secrets.GALAXY_API_KEY }}"
+
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -25,4 +29,4 @@ jobs:
       - name: Run mypy
         run: docker run --rm ${{ steps.build.outputs.imageid }} poetry run mypy .
       - name: Run tests
-        run: docker run --rm ${{ steps.build.outputs.imageid }} poetry run pytest test_examples.py
+        run: docker run --rm -e GALAXY_URL=${{ env.GALAXY_URL }} -e GALAXY_API_KEY=${{ env.GALAXY_API_KEY }} ${{ steps.build.outputs.imageid }} poetry run pytest test_examples.py

Dockerfile

@@ -2,7 +2,10 @@ FROM python:3.13-slim
 
 RUN apt update && apt install -y \
     curl \
-    g++
+    g++ \
+    libosmesa6-dev \
+    libx11-dev \
+    libxrender1
 
 ENV POETRY_HOME=/poetry
 ENV PATH=/poetry/bin:$PATH

README.md

@@ -6,9 +6,22 @@ This repository contains examples of how to build application functionalities in
 
 1. [Creating a form for a Pydantic model](examples/pydantic_form)
 2. [Create a JSON editor for a Pydantic model](examples/pydantic_monaco)
-3. [Working with Plotly](examples/plotly)
-4. [Working with Matplotlib](examples/matplotlib)
-5. [Synchronizing changes between tabs](examples/multitab)
+3. [Conditionally rendering elements](examples/conditional_rendering)
+4. [Conditionally disabling elements](examples/conditional_disabling)
+5. [Changing Pydantic rules based on user input](examples/dynamic_pydantic_rules)
+6. [Complex Pydantic rules](examples/complex_pydantic_rules)
+7. [Selecting datafiles from the server](examples/data_selector)
+8. [Running a Galaxy tool](examples/run_galaxy_tool)
+9. [Running a Galaxy workflow](examples/run_galaxy_workflow)
+10. [Working with Plotly](examples/plotly)
+11. [Working with Matplotlib](examples/matplotlib)
+12. [Working with VTK](examples/vtk)
+13. [Synchronizing changes between tabs](examples/multitab)
+
+We also provide examples that take advantage of ORNL resources:
+
+1. [Selecting datafiles from the Analysis Cluster](examples/ornl/neutron_data_selector)
+2. [Selecting datafiles from ONCat](examples/ornl/oncat)
 
 ## Running Examples
 
@@ -19,11 +32,22 @@ poetry install
 poetry run python examples/{example_folder}/main.py
 ```
 
+## Running Tests
+
+This repo includes an automated test to ensure that each example runs:
+
+```bash
+poetry install
+poetry run pytest
+```
+
+You can set the environment variable `INCLUDE_ORNL_TESTS=1` if you want to test the examples that rely on specific ORNL resources. Note that you will need to run them from a location that has access to these resources.
+
 ## Example Structure
 
-We use the MVVM framework for NOVA applications. With this in mind, each example is broken down into the following files:
+We use the MVVM framework for NOVA applications. With this in mind, each example is broken down into the following sections:
 
-1. view.py - Sets up a Trame GUI for the example.
-2. model.py - Sets up a Pydantic model and any business logic needed by the application.
-3. view_model.py - Sets up a view model that binds the model and view.
+1. view - Sets up a Trame GUI for the example.
+2. model - Sets up a Pydantic model and any business logic needed by the application.
+3. view_model - Sets up a view model that binds the model and view.
 4. main.py - Entrypoint for the Trame GUI.

examples/complex_pydantic_rules/main.py

@@ -0,0 +1,12 @@
+"""Runs the complex Pydantic rules example."""
+
+from examples.complex_pydantic_rules.view import App
+
+
+def main() -> None:
+    app = App()
+    app.server.start(open_browser=False)
+
+
+if __name__ == "__main__":
+    main()

examples/complex_pydantic_rules/model.py

@@ -0,0 +1,51 @@
+"""
+Model implementation for complex Pydantic rules example.
+
+Here, we will create a Pydantic rule to use nltk to clean and tokenize text provided by the user.
+"""
+
+import re
+
+import nltk
+from nltk.corpus import stopwords
+from nltk.tokenize import word_tokenize
+from pydantic import BaseModel, Field, model_validator
+from typing_extensions import Self
+
+
+class FormData(BaseModel):
+    """Pydantic model for the form data."""
+
+    tokenized_text: str = Field(default="", title="Tokenized Text")
+    text: str = Field(default="", title="Input Text")
+
+    # Now, we will leverage Pydantic to clean and tokenize the text.
+    # One could also use a Pydantic computed_field here.
+    @model_validator(mode="after")
+    def tokenize_text(self) -> Self:
+        input_text = self.text.lower()
+
+        # If any field in the model is invalid, then you can raise a ValueError and display the error to the user.
+        if "error" in input_text:
+            raise ValueError("Text must not contain the word error.")
+
+        # Remove punctuation and other non-word text.
+        cleaned_text = re.sub(r"[\W]", " ", input_text)
+
+        # Tokenize the text and remove stopwords.
+        words = word_tokenize(cleaned_text)
+        stop_words = set(stopwords.words("english"))
+        self.tokenized_text = " ".join([word for word in words if word not in stop_words])
+
+        # This is required by Pydantic.
+        return self
+
+
+class Model:
+    """Model implementation for complex Pydantic rules example."""
+
+    def __init__(self) -> None:
+        nltk.download("stopwords")
+        nltk.download("punkt_tab")
+
+        self.form = FormData()

examples/complex_pydantic_rules/view.py

@@ -0,0 +1,41 @@
+"""View for complex Pydantic rules example."""
+
+from nova.mvvm.trame_binding import TrameBinding
+from nova.trame import ThemedApp
+from nova.trame.view.components import InputField
+from nova.trame.view.layouts import VBoxLayout
+from trame.widgets import vuetify3 as vuetify
+
+from .model import Model
+from .view_model import ViewModel
+
+
+class App(ThemedApp):
+    """View for complex Pydantic rules example."""
+
+    def __init__(self) -> None:
+        super().__init__()
+
+        self.create_vm()
+        # If you forget to call connect, then the application will crash when you attempt to update the view.
+        self.view_model.form_data_bind.connect("data")
+        # Generally, we want to initialize the view state before creating the UI for ease of use. If initialization
+        # is expensive, then you can defer it. In this case, you must handle the view state potentially being
+        # uninitialized in the UI via v_if statements.
+        self.view_model.update_form_data()
+
+        self.create_ui()
+
+    def create_ui(self) -> None:
+        with super().create_ui() as layout:
+            with layout.content:
+                with vuetify.VCard(classes="mx-auto my-4", max_width=600):
+                    with VBoxLayout(columns=3, gap="0.5em"):
+                        InputField(v_model="data.text", type="textarea")
+                        InputField(v_model="data.tokenized_text", readonly=True, type="textarea")
+
+    def create_vm(self) -> None:
+        binding = TrameBinding(self.state)
+
+        model = Model()
+        self.view_model = ViewModel(model, binding)

examples/complex_pydantic_rules/view_model.py

@@ -0,0 +1,25 @@
+"""View model implementation for complex Pydantic rules example."""
+
+from typing import Any, Dict
+
+from nova.mvvm.interface import BindingInterface
+
+from .model import Model
+
+
+class ViewModel:
+    """View model implementation for complex Pydantic rules example."""
+
+    def __init__(self, model: Model, binding: BindingInterface) -> None:
+        self.model = model
+
+        # self.on_update is called any time the view updates the binding.
+        self.form_data_bind = binding.new_bind(self.model.form, callback_after_update=self.send_cleaned_text_to_view)
+
+    def send_cleaned_text_to_view(self, results: Dict[str, Any]) -> None:
+        # This is necessary to send the cleaned text to the view since it's updated programmatically.
+        self.form_data_bind.update_in_view(self.model.form)
+
+    def update_form_data(self) -> None:
+        # This will fail if you haven't called connect on the binding!
+        self.form_data_bind.update_in_view(self.model.form)

examples/conditional_disabling/main.py

@@ -0,0 +1,12 @@
+"""Runs the conditional disabling example."""
+
+from examples.conditional_disabling.view import App
+
+
+def main() -> None:
+    app = App()
+    app.server.start(open_browser=False)
+
+
+if __name__ == "__main__":
+    main()

examples/conditional_disabling/model.py

@@ -0,0 +1,19 @@
+"""Model implementation for conditional disabling example."""
+
+from pydantic import BaseModel, Field
+
+
+class FormData(BaseModel):
+    """Pydantic model for the form data."""
+
+    disable_phone_field: bool = Field(default=False, title="Disable Phone Number?")
+    email_address: str = Field(default="", title="Email Address")
+    full_name: str = Field(default="", title="Full Name")
+    phone_number: str = Field(default="", title="Phone Number")
+
+
+class Model:
+    """Model implementation for conditional disabling example."""
+
+    def __init__(self) -> None:
+        self.form = FormData()

examples/conditional_disabling/view.py

@@ -0,0 +1,49 @@
+"""View for conditional disabling example."""
+
+from nova.mvvm.trame_binding import TrameBinding
+from nova.trame import ThemedApp
+from nova.trame.view.components import InputField
+from nova.trame.view.layouts import GridLayout, HBoxLayout
+from trame.widgets import vuetify3 as vuetify
+
+from .model import Model
+from .view_model import ViewModel
+
+
+class App(ThemedApp):
+    """View for conditional disabling example."""
+
+    def __init__(self) -> None:
+        super().__init__()
+
+        self.create_vm()
+        # If you forget to call connect, then the application will crash when you attempt to update the view.
+        self.view_model.form_data_bind.connect("data")
+        # Generally, we want to initialize the view state before creating the UI for ease of use. If initialization
+        # is expensive, then you can defer it. In this case, you must handle the view state potentially being
+        # uninitialized in the UI via v_if statements.
+        self.view_model.update_form_data()
+
+        self.create_ui()
+
+    def create_ui(self) -> None:
+        with super().create_ui() as layout:
+            with layout.content:
+                with vuetify.VCard(classes="mx-auto my-4", max_width=600):
+                    with GridLayout(columns=2, classes="mb-2", gap="0.5em"):
+                        InputField(v_model="data.email_address")
+                        InputField(v_model="data.full_name")
+
+                    with HBoxLayout(gap="0.5em", valign="center"):
+                        InputField(v_model="data.disable_phone_field", type="checkbox")
+
+                        # Now, we can use disable_phone_field to conditionally disable the phone number field.
+                        # Note that because we need to bind to a parameter that doesn't start with v_ (indicating a
+                        # v-directive in Vue.js), we need to use the Trame tuple syntax to bind to disabled.
+                        InputField(v_model="data.phone_number", disabled=("data.disable_phone_field",))
+
+    def create_vm(self) -> None:
+        binding = TrameBinding(self.state)
+
+        model = Model()
+        self.view_model = ViewModel(model, binding)

examples/conditional_disabling/view_model.py

@@ -0,0 +1,19 @@
+"""View model implementation for conditional disabling example."""
+
+from nova.mvvm.interface import BindingInterface
+
+from .model import Model
+
+
+class ViewModel:
+    """View model implementation for conditional disabling example."""
+
+    def __init__(self, model: Model, binding: BindingInterface) -> None:
+        self.model = model
+
+        # self.on_update is called any time the view updates the binding.
+        self.form_data_bind = binding.new_bind(self.model.form)
+
+    def update_form_data(self) -> None:
+        # This will fail if you haven't called connect on the binding!
+        self.form_data_bind.update_in_view(self.model.form)

examples/conditional_rendering/main.py

@@ -0,0 +1,12 @@
+"""Runs the conditional rendering example."""
+
+from examples.conditional_rendering.view import App
+
+
+def main() -> None:
+    app = App()
+    app.server.start(open_browser=False)
+
+
+if __name__ == "__main__":
+    main()

examples/conditional_rendering/model.py

@@ -0,0 +1,24 @@
+"""Model implementation for conditional rendering example."""
+
+from pydantic import BaseModel, Field
+
+
+class FormData(BaseModel):
+    """Pydantic model for the form data."""
+
+    comments: str = Field(default="", title="Comments")
+    email_address: str = Field(default="", title="Email Address")
+    full_name: str = Field(default="", title="Full Name")
+    phone_number: str = Field(default="", title="Phone Number")
+    show_phone_field: bool = Field(default=False, title="Add Phone Number?")
+    show_comments_field: bool = Field(default=False)
+
+
+class Model:
+    """Model implementation for conditional rendering example."""
+
+    def __init__(self) -> None:
+        self.form = FormData()
+
+    def toggle_comments(self) -> None:
+        self.form.show_comments_field = not self.form.show_comments_field