Web UI - stage1, readonly part (#606)

* added fastapi as web ui backend

* Added cube + benchmark basic listing

* Adds navigation

* Aded mlcube detailed page

* Improved mlcubes detailed layout

* Improved mlcube layout

* yaml displaying

* yaml: spinner

* yaml panel improvement

* yaml panel layout improvement

* layout fixes

* Added benchmark detailed page

* added links to mlcube

* benchmark page: added owner

* Colors refactoring

* Dataset detailed page

* Forgot to add js file

* Unified data format for all data fields automatically

* (mlcube-detailed) Display image tarball and additional files always

* Fixed scrolling and reinvented basic page layout

* Fix navbar is hiding

* Make templates & static files independent of user's workdir

* Added error handling

* Display invalid entities correctly

* Added invalid entities highlighting + badges

* Added benchmark associations

* Improved association panel style

* Added association card

* Sorted associations by status / timestamp

* Sorted mlcubes and datasets: mine first

* Added associations to dataset page

* Added associations to mlcube page

* Refactored details page - extracted common styles to the base template

* Refactored association sorting  to common util

* Display my benchmarks first

* Hid empty links

* Mlcube-as-a-link unified view

* resources.path cannot return a dir with subdirs for py3.9

* Fixed resources path for templates also

* linter fix

* static local resources instead of remote ones

* layout fix: align mlcubes vertically

* bugfix: add some dependencies for isolated run

* Fixes after merging main

* MedperfSchema requires a name field

* Linter fix

* Pass mlcube params instead of url

* Pass mlcube parameters to fetch-yaml

---------

Co-authored-by: Alejandro Aristizabal <[email protected]>

cli/medperf/cli.py

@@ -17,6 +17,7 @@
 import medperf.commands.association.association as association
 import medperf.commands.compatibility_test.compatibility_test as compatibility_test
 import medperf.commands.storage as storage
+import medperf.web_ui.app as web_ui
 from medperf.utils import check_for_updates
 from medperf.logging.utils import log_machine_details
 
@@ -30,6 +31,7 @@
 app.add_typer(compatibility_test.app, name="test", help="Manage compatibility tests")
 app.add_typer(auth.app, name="auth", help="Authentication")
 app.add_typer(storage.app, name="storage", help="Storage management")
+app.add_typer(web_ui.app, name="web-ui", help="local web UI to manage medperf entities")
 
 
 @app.command("run")

cli/medperf/commands/list.py

@@ -19,6 +19,8 @@ def run(
         """Lists all local datasets
 
         Args:
+            entity_class: entity class to instantiate (Dataset, Model, etc.)
+            fields (list[str]): list of fields to display
             unregistered (bool, optional): Display only local unregistered results. Defaults to False.
             mine_only (bool, optional): Display all registered current-user results. Defaults to False.
             kwargs (dict): Additional parameters for filtering entity lists.

cli/medperf/entities/association.py

@@ -0,0 +1,16 @@
+from datetime import datetime
+from typing import Optional
+
+from medperf.entities.schemas import ApprovableSchema, MedperfSchema
+
+
+class Association(MedperfSchema, ApprovableSchema):
+    id: int
+    metadata: dict
+    dataset: Optional[int]
+    model_mlcube: Optional[int]
+    benchmark: int
+    initiated_by: int
+    created_at: Optional[datetime]
+    modified_at: Optional[datetime]
+    name: str = "Association"  # The server data doesn't have name, while MedperfSchema requires it

cli/medperf/entities/benchmark.py

@@ -2,6 +2,7 @@
 from pydantic import HttpUrl, Field
 
 import medperf.config as config
+from medperf.entities.association import Association
 from medperf.entities.interface import Entity
 from medperf.entities.schemas import ApprovableSchema, DeployableSchema
 from medperf.account_management import get_medperf_user_data
@@ -83,7 +84,6 @@ def get_models_uids(cls, benchmark_uid: int) -> List[int]:
 
         Args:
             benchmark_uid (int): UID of the benchmark.
-            comms (Comms): Instance of the communications interface.
 
         Returns:
             List[int]: List of mlcube uids
@@ -96,6 +96,36 @@ def get_models_uids(cls, benchmark_uid: int) -> List[int]:
         ]
         return models_uids
 
+    @classmethod
+    def get_models_associations(cls, benchmark_uid: int) -> List[Association]:
+        """Retrieves the list of model associations to the benchmark
+
+        Args:
+            benchmark_uid (int): UID of the benchmark.
+
+        Returns:
+            List[Association]: List of associations
+        """
+        associations = config.comms.get_cubes_associations()
+        associations = [Association(**assoc) for assoc in associations]
+        associations = [a for a in associations if a.benchmark == benchmark_uid]
+        return associations
+
+    @classmethod
+    def get_datasets_associations(cls, benchmark_uid: int) -> List[Association]:
+        """Retrieves the list of models associated to the benchmark
+
+        Args:
+            benchmark_uid (int): UID of the benchmark.
+
+        Returns:
+            List[Association]: List of associations
+        """
+        associations = config.comms.get_datasets_associations()
+        associations = [Association(**assoc) for assoc in associations]
+        associations = [a for a in associations if a.benchmark == benchmark_uid]
+        return associations
+
     def display_dict(self):
         return {
             "UID": self.identifier,

cli/medperf/entities/cube.py

@@ -1,10 +1,11 @@
 import os
 import yaml
 import logging
-from typing import Dict, Optional, Union
+from typing import Dict, Optional, Union, List
 from pydantic import Field
 from pathlib import Path
 
+from medperf.entities.association import Association
 from medperf.utils import (
     combine_proc_sp_text,
     log_storage,
@@ -96,19 +97,20 @@ def remote_prefilter(filters: dict):
         return comms_fn
 
     @classmethod
-    def get(cls, cube_uid: Union[str, int], local_only: bool = False) -> "Cube":
+    def get(cls, cube_uid: Union[str, int], local_only: bool = False, valid_only: bool = True) -> "Cube":
         """Retrieves and creates a Cube instance from the comms. If cube already exists
         inside the user's computer then retrieves it from there.
 
         Args:
+            valid_only: if to raise an error in case of invalidated Cube
             cube_uid (str): UID of the cube.
 
         Returns:
             Cube : a Cube instance with the retrieved data.
         """
 
         cube = super().get(cube_uid, local_only)
-        if not cube.is_valid:
+        if not cube.is_valid and valid_only:
             raise InvalidEntityError("The requested MLCube is marked as INVALID.")
         cube.download_config_files()
         return cube
@@ -152,7 +154,7 @@ def download_image(self):
                 # For singularity, we need the hash first before trying to convert
                 self._set_image_hash_from_registry()
 
-                image_folder = os.path.join(config.cubes_folder, config.image_path)
+                image_folder: str = os.path.join(config.cubes_folder, config.image_path)
                 if os.path.exists(image_folder):
                     for file in os.listdir(image_folder):
                         if file == self._converted_singularity_image_name:
@@ -198,7 +200,7 @@ def _get_image_from_registry(self):
             cmd += f" -Psingularity.image={self._converted_singularity_image_name}"
         logging.info(f"Running MLCube command: {cmd}")
         with spawn_and_kill(
-            cmd, timeout=config.mlcube_configure_timeout
+                cmd, timeout=config.mlcube_configure_timeout
         ) as proc_wrapper:
             proc = proc_wrapper.proc
             combine_proc_sp_text(proc)
@@ -228,13 +230,13 @@ def download_run_files(self):
             raise InvalidEntityError(f"MLCube {self.name} image file: {e}")
 
     def run(
-        self,
-        task: str,
-        output_logs: str = None,
-        string_params: Dict[str, str] = {},
-        timeout: int = None,
-        read_protected_input: bool = True,
-        **kwargs,
+            self,
+            task: str,
+            output_logs: str = None,
+            string_params: Dict[str, str] = {},
+            timeout: int = None,
+            read_protected_input: bool = True,
+            **kwargs,
     ):
         """Executes a given task on the cube instance
 
@@ -358,6 +360,22 @@ def get_config(self, identifier):
 
         return cube
 
+    @classmethod
+    def get_benchmarks_associations(cls, mlcube_uid: int) -> List[Association]:
+        """Retrieves the list of benchmarks model is associated with
+
+        Args:
+            mlcube_uid (int): UID of the cube.
+            comms (Comms): Instance of the communications interface.
+
+        Returns:
+            List[Association]: List of associations
+        """
+        associations = config.comms.get_cubes_associations()
+        associations = [Association(**assoc) for assoc in associations]
+        associations = [a for a in associations if a.model_mlcube == mlcube_uid]
+        return associations
+
     def display_dict(self):
         return {
             "UID": self.identifier,

cli/medperf/entities/dataset.py

@@ -1,8 +1,9 @@
 import os
 import yaml
 from pydantic import Field, validator
-from typing import Optional, Union
+from typing import Optional, Union, List
 
+from medperf.entities.association import Association
 from medperf.utils import remove_path
 from medperf.entities.interface import Entity
 from medperf.entities.schemas import DeployableSchema
@@ -112,14 +113,27 @@ def remote_prefilter(filters: dict) -> callable:
             comms_fn = config.comms.get_user_datasets
 
         if "mlcube" in filters and filters["mlcube"] is not None:
-
             def func():
                 return config.comms.get_mlcube_datasets(filters["mlcube"])
 
             comms_fn = func
 
         return comms_fn
 
+    @classmethod
+    def get_benchmarks_associations(cls, dataset_uid: int) -> List[Association]:
+        """Retrieves the list of benchmarks dataset is associated with
+
+        Args:
+            dataset_uid (int): UID of the dataset.
+        Returns:
+            List[Association]: List of associations
+        """
+        associations = config.comms.get_datasets_associations()
+        associations = [Association(**assoc) for assoc in associations]
+        associations = [a for a in associations if a.dataset == dataset_uid]
+        return associations
+
     def display_dict(self):
         return {
             "UID": self.identifier,

cli/medperf/entities/interface.py

@@ -50,7 +50,7 @@ def path(self) -> str:
 
     @classmethod
     def all(
-        cls: Type[EntityType], unregistered: bool = False, filters: dict = {}
+            cls: Type[EntityType], unregistered: bool = False, filters: dict = {}
     ) -> List[EntityType]:
         """Gets a list of all instances of the respective entity.
         Whether the list is local or remote depends on the implementation.
@@ -112,7 +112,7 @@ def remote_prefilter(filters: dict) -> callable:
 
     @classmethod
     def get(
-        cls: Type[EntityType], uid: Union[str, int], local_only: bool = False
+            cls: Type[EntityType], uid: Union[str, int], local_only: bool = False, valid_only: bool = True
     ) -> EntityType:
         """Gets an instance of the respective entity.
         Wether this requires only local read or remote calls depends
@@ -121,6 +121,7 @@ def get(
         Args:
             uid (str): Unique Identifier to retrieve the entity
             local_only (bool): If True, the entity will be retrieved locally
+            valid_only: if to raise en error in case of invalidated entity
 
         Returns:
             Entity: Entity Instance associated to the UID

cli/medperf/entities/report.py

@@ -73,15 +73,16 @@ def all(cls, unregistered: bool = False, filters: dict = {}) -> List["TestReport
         return super().all(unregistered=True, filters={})
 
     @classmethod
-    def get(cls, uid: str, local_only: bool = False) -> "TestReport":
+    def get(cls, uid: str, local_only: bool = False, valid_only: bool = True) -> "TestReport":
         """Gets an instance of the TestReport. ignores local_only inherited flag as TestReport is always a local entity.
         Args:
             uid (str): Report Unique Identifier
             local_only (bool): ignored. Left for aligning with parent Entity class
+            valid_only: if to raise an error in case of invalidated entity
         Returns:
             TestReport: Report Instance associated to the UID
         """
-        return super().get(uid, local_only=True)
+        return super().get(uid, local_only=True, valid_only=valid_only)
 
     def display_dict(self):
         if self.data_path:

cli/medperf/web_ui/app.py

@@ -0,0 +1,50 @@
+from importlib import resources
+from pathlib import Path
+
+import typer
+from fastapi import FastAPI
+from fastapi.responses import RedirectResponse
+from fastapi.staticfiles import StaticFiles
+
+from medperf import config
+from medperf.decorators import clean_except
+from medperf.web_ui.common import custom_exception_handler
+from medperf.web_ui.datasets.routes import router as datasets_router
+from medperf.web_ui.benchmarks.routes import router as benchmarks_router
+from medperf.web_ui.mlcubes.routes import router as mlcubes_router
+from medperf.web_ui.yaml_fetch.routes import router as yaml_fetch_router
+
+web_app = FastAPI()
+
+web_app.include_router(datasets_router, prefix="/datasets")
+web_app.include_router(benchmarks_router, prefix="/benchmarks")
+web_app.include_router(mlcubes_router, prefix="/mlcubes")
+web_app.include_router(yaml_fetch_router)
+
+static_folder_path = Path(resources.files("medperf.web_ui")) / "static"  # noqa
+web_app.mount(
+    "/static",
+    StaticFiles(
+        directory=static_folder_path,
+    )
+)
+
+web_app.add_exception_handler(Exception, custom_exception_handler)
+
+
+@web_app.get("/", include_in_schema=False)
+def read_root():
+    return RedirectResponse(url="/benchmarks/ui")
+
+
+app = typer.Typer()
+
+
+@app.command("run")
+@clean_except
+def run(
+        port: int = typer.Option(8100, "--port", help="port to use"),
+):
+    """Runs a local web UI"""
+    import uvicorn
+    uvicorn.run(web_app, host="127.0.0.1", port=port, log_level=config.loglevel)

cli/medperf/web_ui/benchmarks/routes.py

@@ -0,0 +1,65 @@
+import logging
+
+from fastapi import APIRouter
+from fastapi.responses import HTMLResponse
+from fastapi import Request
+
+from medperf.entities.benchmark import Benchmark
+from medperf.entities.dataset import Dataset
+from medperf.entities.cube import Cube
+from medperf.account_management import get_medperf_user_data
+from medperf.web_ui.common import templates, sort_associations_display
+
+router = APIRouter()
+logger = logging.getLogger(__name__)
+
+
+@router.get("/ui", response_class=HTMLResponse)
+def benchmarks_ui(request: Request, mine_only: bool = False):
+    filters = {}
+    my_user_id = get_medperf_user_data()["id"]
+    if mine_only:
+        filters["owner"] = my_user_id
+
+    benchmarks = Benchmark.all(
+        filters=filters,
+    )
+
+    benchmarks = sorted(benchmarks, key=lambda x: x.created_at, reverse=True)
+    # sort by (mine recent) (mine oldish), (other recent), (other oldish)
+    mine_benchmarks = [d for d in benchmarks if d.owner == my_user_id]
+    other_benchmarks = [d for d in benchmarks if d.owner != my_user_id]
+    benchmarks = mine_benchmarks + other_benchmarks
+    return templates.TemplateResponse("benchmarks.html", {"request": request, "benchmarks": benchmarks})
+
+
+@router.get("/ui/{benchmark_id}", response_class=HTMLResponse)
+def benchmark_detail_ui(request: Request, benchmark_id: int):
+    benchmark = Benchmark.get(benchmark_id)
+    data_preparation_mlcube = Cube.get(cube_uid=benchmark.data_preparation_mlcube)
+    reference_model_mlcube = Cube.get(cube_uid=benchmark.reference_model_mlcube)
+    metrics_mlcube = Cube.get(cube_uid=benchmark.data_evaluator_mlcube)
+    datasets_associations = Benchmark.get_datasets_associations(benchmark_uid=benchmark_id)
+    models_associations = Benchmark.get_models_associations(benchmark_uid=benchmark_id)
+
+    datasets_associations = sort_associations_display(datasets_associations)
+    models_associations = sort_associations_display(models_associations)
+
+    datasets = {assoc.dataset: Dataset.get(assoc.dataset) for assoc in datasets_associations if assoc.dataset}
+    models = {assoc.model_mlcube: Cube.get(assoc.model_mlcube) for assoc in models_associations if assoc.model_mlcube}
+
+    return templates.TemplateResponse(
+        "benchmark_detail.html",
+        {
+            "request": request,
+            "entity": benchmark,
+            "entity_name": benchmark.name,
+            "data_preparation_mlcube": data_preparation_mlcube,
+            "reference_model_mlcube": reference_model_mlcube,
+            "metrics_mlcube": metrics_mlcube,
+            "datasets_associations": datasets_associations,
+            "models_associations": models_associations,
+            "datasets": datasets,
+            "models": models
+        }
+    )