Web UI

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/dataset/associate.py

@@ -1,7 +1,7 @@
 from medperf import config
 from medperf.entities.dataset import Dataset
 from medperf.entities.benchmark import Benchmark
-from medperf.utils import dict_pretty_print, approval_prompt
+from medperf.utils import dict_pretty_format, approval_prompt
 from medperf.commands.result.create import BenchmarkExecution
 from medperf.exceptions import InvalidArgumentError
 
@@ -38,7 +38,7 @@ def run(data_uid: int, benchmark_uid: int, approved=False, no_cache=False):
         ui.print("These are the results generated by the compatibility test. ")
         ui.print("This will be sent along the association request.")
         ui.print("They will not be part of the benchmark.")
-        dict_pretty_print(result.results)
+        ui.print(dict_pretty_format(result.results))
 
         msg = "Please confirm that you would like to associate"
         msg += f" the dataset {dset.name} with the benchmark {benchmark.name}."

cli/medperf/commands/dataset/dataset.py

@@ -1,3 +1,5 @@
+import logging
+
 import typer
 from typing import Optional
 

cli/medperf/commands/dataset/prepare.py

@@ -4,7 +4,7 @@
 from medperf.entities.dataset import Dataset
 import medperf.config as config
 from medperf.entities.cube import Cube
-from medperf.utils import approval_prompt, dict_pretty_print
+from medperf.utils import approval_prompt, dict_pretty_format
 from medperf.exceptions import (
     CommunicationError,
     ExecutionError,
@@ -279,6 +279,8 @@ def __generate_report_dict(self):
             with open(self.report_path, "r") as f:
                 report_dict = yaml.safe_load(f)
 
+            # TODO: this specific logic with status is very tuned to the RANO. Hope we'd
+            #  make it more general once
             report = pd.DataFrame(report_dict)
             if "status" in report.keys():
                 report_status = report.status.value_counts() / len(report)
@@ -290,15 +292,16 @@ def __generate_report_dict(self):
 
         return report_status_dict
 
-    def prompt_for_report_sending_approval(self):
+    @staticmethod
+    def _report_sending_approval_msg():
         example = {
             "execution_status": "running",
             "progress": {
                 "Stage 1": "40%",
                 "Stage 3": "60%",
             },
         }
-
+        result = []
         msg = (
             "\n=================================================\n"
             + "During preparation, each subject of your dataset will undergo multiple"
@@ -312,8 +315,8 @@ def prompt_for_report_sending_approval(self):
             + " dataset subjects have reached Stage 1, and that 60% of your dataset subjects"
             + " have reached Stage 3:"
         )
-        config.ui.print(msg)
-        dict_pretty_print(example)
+        result.append(msg)
+        result.append(dict_pretty_format(example))
 
         msg = (
             "\nYou can decide whether or not to send information about your dataset preparation"
@@ -323,8 +326,11 @@ def prompt_for_report_sending_approval(self):
             + "\nsubmission of summaries similar to the one above to the MedPerf Server throughout"
             + "\nthe preparation process?[Y/n]"
         )
+        result.append(msg)
+        return '\n'.join(result)
 
-        self.allow_sending_reports = approval_prompt(msg)
+    def prompt_for_report_sending_approval(self):
+        self.allow_sending_reports = approval_prompt(self._report_sending_approval_msg())
 
     def send_report(self, report_metadata):
         # Since we don't actually need concurrency, let's have

cli/medperf/commands/dataset/set_operational.py

@@ -1,6 +1,6 @@
 from medperf.entities.dataset import Dataset
 import medperf.config as config
-from medperf.utils import approval_prompt, dict_pretty_print, get_folders_hash
+from medperf.utils import approval_prompt, dict_pretty_format, get_folders_hash
 from medperf.exceptions import CleanExit, InvalidArgumentError
 import yaml
 
@@ -51,7 +51,7 @@ def set_operational(self):
 
     def update(self):
         body = self.todict()
-        dict_pretty_print(body)
+        self.ui.print(dict_pretty_format(body))
         msg = "Do you approve sending the presented data to MedPerf? [Y/n] "
         self.approved = self.approved or approval_prompt(msg)
 

cli/medperf/commands/dataset/submit.py

@@ -7,7 +7,7 @@
 from medperf.entities.benchmark import Benchmark
 from medperf.utils import (
     approval_prompt,
-    dict_pretty_print,
+    dict_pretty_format,
     get_folders_hash,
     remove_path,
 )
@@ -43,11 +43,17 @@
             submit_as_prepared,
             for_test,
         )
-        preparation.validate()
-        preparation.validate_prep_cube()
-        preparation.create_dataset_object()
-        if submit_as_prepared:
-            preparation.make_dataset_prepared()
+        submission_dict = preparation.prepare_dict(submit_as_prepared)
+        config.ui.print(dict_pretty_format(submission_dict))
+
+        msg = "Do you approve the registration of the presented data to MedPerf? [Y/n] "
+        warning = (
+            "Upon submission, your email address will be visible to the Data Preparation"
+            + " Owner for traceability and debugging purposes."
+        )
+        config.ui.print_warning(warning)
+        preparation.approved = preparation.approved or approval_prompt(msg)
+
         updated_dataset_dict = preparation.upload()
         preparation.to_permanent_path(updated_dataset_dict)
         preparation.write(updated_dataset_dict)
@@ -69,8 +75,8 @@
         for_test: bool,
     ):
         self.ui = config.ui
         self.data_path = str(Path(data_path).resolve())
         self.labels_path = str(Path(labels_path).resolve())
         self.metadata_path = metadata_path
         self.name = name
         self.description = description
@@ -82,9 +88,9 @@
         self.for_test = for_test
 
     def validate(self):
         if not os.path.exists(self.data_path):
             raise InvalidArgumentError("The provided data path doesn't exist")
         if not os.path.exists(self.labels_path):
             raise InvalidArgumentError("The provided labels path doesn't exist")
 
         if not self.submit_as_prepared and self.metadata_path:
@@ -137,8 +143,8 @@
         self.dataset = dataset
 
     def make_dataset_prepared(self):
         shutil.copytree(self.data_path, self.dataset.data_path)
         shutil.copytree(self.labels_path, self.dataset.labels_path)
         if self.metadata_path:
             shutil.copytree(self.metadata_path, self.dataset.metadata_path)
         else:
@@ -147,17 +153,16 @@
             # have prepared datasets with no the metadata information
             os.makedirs(self.dataset.metadata_path, exist_ok=True)
 
-    def upload(self):
-        submission_dict = self.dataset.todict()
-        dict_pretty_print(submission_dict)
-        msg = "Do you approve the registration of the presented data to MedPerf? [Y/n] "
-        warning = (
-            "Upon submission, your email address will be visible to the Data Preparation"
-            + " Owner for traceability and debugging purposes."
-        )
-        self.ui.print_warning(warning)
-        self.approved = self.approved or approval_prompt(msg)
+    def prepare_dict(self, submit_as_prepared: bool):
+        self.validate()
+        self.validate_prep_cube()
+        self.create_dataset_object()
+        if submit_as_prepared:
+            self.make_dataset_prepared()
 
+        return self.dataset.todict()
+
+    def upload(self):
         if self.approved:
             updated_body = self.dataset.upload()
             return updated_body

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/commands/mlcube/associate.py

@@ -1,7 +1,7 @@
 from medperf import config
 from medperf.entities.cube import Cube
 from medperf.entities.benchmark import Benchmark
-from medperf.utils import dict_pretty_print, approval_prompt
+from medperf.utils import dict_pretty_format, approval_prompt
 from medperf.commands.compatibility_test.run import CompatibilityTestExecution
 
 
@@ -32,7 +32,7 @@ def run(
         ui.print("These are the results generated by the compatibility test. ")
         ui.print("This will be sent along the association request.")
         ui.print("They will not be part of the benchmark.")
-        dict_pretty_print(results)
+        ui.print(dict_pretty_format(results))
 
         msg = "Please confirm that you would like to associate "
         msg += f"the MLCube '{cube.name}' with the benchmark '{benchmark.name}' [Y/n]"

cli/medperf/commands/profile.py

@@ -2,7 +2,7 @@
 
 from medperf import config
 from medperf.decorators import configurable, clean_except
-from medperf.utils import dict_pretty_print
+from medperf.utils import dict_pretty_format
 from medperf.config_management import read_config, write_config
 from medperf.exceptions import InvalidArgumentError
 
@@ -86,7 +86,7 @@ def view(profile: str = typer.Argument(None)):
     profile_config.pop(config.credentials_keyword, None)
     profile_name = profile if profile else config_p.active_profile_name
     config.ui.print(f"\nProfile '{profile_name}':")
-    dict_pretty_print(profile_config, skip_none_values=False)
+    config.ui.print(dict_pretty_format(profile_config, skip_none_values=False))
 
 
 @app.command("delete")

cli/medperf/commands/result/create.py

@@ -1,4 +1,5 @@
 import os
+import time
 from typing import List, Optional
 from medperf.account_management.account_management import get_medperf_user_data
 from medperf.commands.execution import Execution
@@ -29,7 +30,7 @@ def run(
         ignore_failed_experiments=False,
         no_cache=False,
         show_summary=False,
-    ):
+    ) -> list[Result]:
         """Benchmark execution flow.
 
         Args:
@@ -164,7 +165,7 @@ def __get_cube(self, uid: int, name: str) -> Cube:
         self.ui.print(f"> {name} cube download complete")
         return cube
 
-    def run_experiments(self):
+    def run_experiments(self) -> list[Result]:
         for model_uid in self.models_uids:
             if model_uid in self.cached_results:
                 self.experiments.append(

cli/medperf/commands/result/submit.py

@@ -1,7 +1,7 @@
 import os
 
 from medperf.exceptions import CleanExit
-from medperf.utils import remove_path, dict_pretty_print, approval_prompt
+from medperf.utils import remove_path, dict_pretty_format, approval_prompt
 from medperf.entities.result import Result
 from medperf import config
 
@@ -25,7 +25,7 @@ def get_result(self):
         self.result = Result.get(self.result_uid)
 
     def request_approval(self):
-        dict_pretty_print(self.result.results)
+        self.ui.print(dict_pretty_format(self.result.results))
         self.ui.print("Above are the results generated by the model")
 
         approved = approval_prompt(
@@ -56,6 +56,8 @@ def to_permanent_path(self, result_dict: dict):
         remove_path(new_result_loc)
         os.rename(old_result_loc, new_result_loc)
 
+
+
     def write(self, updated_result_dict):
         result = Result(**updated_result_dict)
         result.write()

cli/medperf/comms/interface.py

@@ -205,7 +205,7 @@ def upload_result(self, results_dict: dict) -> int:
         """
 
     @abstractmethod
-    def associate_dset(self, data_uid: int, benchmark_uid: int, metadata: dict = {}):
+    def associate_dset(self, data_uid: int, benchmark_uid: int, metadata: dict = {}) -> None:
         """Create a Dataset Benchmark association
 
         Args:

cli/medperf/comms/rest.py

@@ -390,7 +390,7 @@ def upload_result(self, results_dict: dict) -> int:
             raise CommunicationRequestError(f"Could not upload the results: {details}")
         return res.json()
 
-    def associate_dset(self, data_uid: int, benchmark_uid: int, metadata: dict = {}):
+    def associate_dset(self, data_uid: int, benchmark_uid: int, metadata: dict = {}) -> None:
         """Create a Dataset Benchmark association
 
         Args:
@@ -515,6 +515,7 @@ def update_dataset(self, dataset_id: int, data: dict):
         res = self.__auth_put(url, json=data)
         if res.status_code != 200:
             log_response_error(res)
+            # TODO: Django returns the error of UNIQUE constraint as a html page
             details = format_errors_dict(res.json())
             raise CommunicationRequestError(f"Could not update dataset: {details}")
         return res.json()

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,