From afe060623d1b2bb9acfec099fe2cc9b8ce8401b6 Mon Sep 17 00:00:00 2001
From: Edan Bainglass <edan.bainglass@gmail.com>
Date: Mon, 4 Sep 2023 05:44:41 +0000
Subject: [PATCH 1/8] Add protocol selector widget

---
 aurora/common/models/battery_experiment.py |  52 ++-
 aurora/experiment/protocols/__init__.py    |   2 +
 aurora/experiment/protocols/selector.py    | 428 +++++++++++++++++++++
 3 files changed, 481 insertions(+), 1 deletion(-)
 create mode 100644 aurora/experiment/protocols/selector.py

diff --git a/aurora/common/models/battery_experiment.py b/aurora/common/models/battery_experiment.py
index 0fe5a6ae..25aa6ab6 100644
--- a/aurora/common/models/battery_experiment.py
+++ b/aurora/common/models/battery_experiment.py
@@ -1,6 +1,6 @@
 import json
 import logging
-from typing import List, Optional, Union
+from typing import Dict, List, Optional, Union
 
 import pandas as pd
 from aiida_aurora.schemas.battery import (BatterySampleJsonTypes,
@@ -41,6 +41,8 @@ def __init__(self):
 
         self.selected_samples = pd.DataFrame()
         self.selected_protocol = ElectroChemSequence(method=[])
+        self.selected_protocols: Dict[int, ElectroChemSequence] = {}
+
         self.add_protocol_step()  # initialize sequence with first default step
 
     def reset_inputs(self):
@@ -368,6 +370,10 @@ def display_query_results(self, query: dict) -> None:
     # ----------------------------------------------------------------------#
     # METHODS RELATED TO PROTOCOLS
     # ----------------------------------------------------------------------#
+    def reset_selected_protocols(self):
+        """Resets all inputs."""
+        self.selected_protocols = {}
+
     def _count_technique_occurencies(self, technique):
         return [type(step)
                 for step in self.selected_protocol.method].count(technique)
@@ -428,6 +434,50 @@ def save_protocol(self):
         except OSError as err:
             print(f"Failed to save protocols => '{str(err)}'")
 
+    def add_selected_protocols(self, indices: List[int]) -> None:
+        """Add selected protocols to local cache.
+
+        Parameters
+        ----------
+        `indices` : `List[int]`
+            The `SelectMultiple` indices of the selected protocols.
+        """
+        for index in indices:
+            self.add_selected_protocol(index)
+
+    def add_selected_protocol(self, index: int) -> None:
+        """Add selected protocol to local cache.
+
+        Parameters
+        ----------
+        `index` : `int`
+             The `SelectMultiple` index of the selected protocol.
+        """
+        if index not in self.selected_protocols:
+            self.selected_protocols[index] = self.available_protocols[index]
+
+    def remove_selected_protocols(self, indices: List[int]) -> None:
+        """Remove selected protocol from local cache.
+
+        Parameters
+        ----------
+        `index` : `int`
+             The `SelectMultiple` index of the selected protocol.
+        """
+        for index in indices:
+            self.remove_selected_protocol(index)
+
+    def remove_selected_protocol(self, index: int) -> None:
+        """Remove selected protocol from local cache.
+
+        Parameters
+        ----------
+        `index` : `int`
+             The `SelectMultiple` index of the selected protocol.
+        """
+        if index in self.selected_protocols:
+            del self.selected_protocols[index]
+
     def update_available_protocols(
         self,
         source_file=AVAILABLE_PROTOCOLS_FILE,
diff --git a/aurora/experiment/protocols/__init__.py b/aurora/experiment/protocols/__init__.py
index 3a44a647..450198a4 100644
--- a/aurora/experiment/protocols/__init__.py
+++ b/aurora/experiment/protocols/__init__.py
@@ -1,7 +1,9 @@
 from .custom import CyclingCustom
+from .selector import ProtocolSelector
 from .standard import CyclingStandard
 
 __all__ = [
     "CyclingCustom",
+    "ProtocolSelector",
     "CyclingStandard",
 ]
diff --git a/aurora/experiment/protocols/selector.py b/aurora/experiment/protocols/selector.py
new file mode 100644
index 00000000..07dd8563
--- /dev/null
+++ b/aurora/experiment/protocols/selector.py
@@ -0,0 +1,428 @@
+from typing import Callable, List, Tuple
+
+import ipywidgets as ipw
+from aiida_aurora.schemas.cycling import (ElectroChemPayloads,
+                                          ElectroChemSequence)
+
+from aurora.common.models.battery_experiment import BatteryExperimentModel
+
+
+class ProtocolSelector(ipw.VBox):
+    """
+    docstring
+    """
+
+    LABEL_LAYOUT = {
+        'margin': '0 auto',
+    }
+
+    CONTROLS_LAYOUT = {
+        'width': '80px',
+    }
+
+    BUTTON_LAYOUT = {
+        'width': '35px',
+        'margin': '5px auto',
+    }
+
+    BOX_STYLE = {
+        'description_width': '5%',
+    }
+
+    BOX_LAYOUT = {
+        'flex': '1',
+    }
+
+    def __init__(
+        self,
+        experiment_model: BatteryExperimentModel,
+        validate_callback_f: Callable,
+    ) -> None:
+        """docstring"""
+
+        if not callable(validate_callback_f):
+            raise TypeError(
+                "validate_callback_f should be a callable function")
+
+        self.experiment_model = experiment_model
+
+        selection_container = self._build_selection_container()
+
+        self.w_validate = ipw.Button(
+            style={
+                'description_width': '30%',
+            },
+            layout={
+                'margin': '5px',
+            },
+            description="Validate",
+            button_style='success',
+            tooltip="Validate the selected sample",
+            icon='check',
+            disabled=True,
+        )
+
+        self.reset_button = ipw.Button(
+            layout={},
+            style={},
+            description="Reset",
+            button_style='danger',
+            tooltip="Clear selection",
+            icon='times',
+        )
+
+        super().__init__(
+            layout={},
+            children=[
+                selection_container,
+                ipw.HBox(
+                    layout={
+                        "align_items": "center",
+                    },
+                    children=[
+                        self.w_validate,
+                        self.reset_button,
+                    ],
+                ),
+            ],
+        )
+
+        self._initialize_selectors()
+
+        self._set_event_listeners(validate_callback_f)
+
+    @property
+    def selected_protocols(self) -> List[ElectroChemSequence]:
+        """docstring"""
+        ids = get_ids(self.w_selected_list.options)
+        return self.experiment_model.query_available_protocols(ids)
+
+    #########
+    # widgets
+    #########
+
+    def _build_selection_container(self) -> ipw.HBox:
+        """docstring"""
+
+        selection_section = self._build_selection_section()
+
+        deselection_section = self._build_selected_section()
+
+        self.selection_details = ipw.Tab(layout={
+            "width": "50%",
+            "max_height": "338px",
+        })
+
+        return ipw.HBox(
+            layout={
+                'width': 'auto',
+                'margin': '2px',
+                'padding': '10px',
+                'border': 'solid darkgrey 1px'
+            },
+            children=[
+                ipw.VBox(
+                    layout={
+                        "width": "50%",
+                    },
+                    children=[
+                        selection_section,
+                        deselection_section,
+                    ],
+                ),
+                self.selection_details,
+            ],
+        )
+
+    def _build_selection_section(self) -> ipw.VBox:
+        """docstring"""
+
+        w_selection_label = ipw.HTML(
+            value="Protocol:",
+            layout=self.LABEL_LAYOUT,
+        )
+
+        selection_controls = self._build_selection_controls()
+
+        self.w_protocol_list = ipw.SelectMultiple(
+            rows=10,
+            style=self.BOX_STYLE,
+            layout=self.BOX_LAYOUT,
+        )
+
+        return ipw.VBox(
+            layout={},
+            children=[
+                ipw.HBox(
+                    layout={},
+                    children=[
+                        ipw.VBox(
+                            layout=self.CONTROLS_LAYOUT,
+                            children=[
+                                w_selection_label,
+                                selection_controls,
+                            ],
+                        ),
+                        self.w_protocol_list,
+                    ],
+                ),
+            ],
+        )
+
+    def _build_selection_controls(self) -> ipw.VBox:
+        """docstring"""
+
+        self.w_update = ipw.Button(
+            description="",
+            button_style='',
+            tooltip="Update available samples",
+            icon='refresh',
+            layout=self.BUTTON_LAYOUT,
+        )
+
+        self.w_select = ipw.Button(
+            description="",
+            button_style='',
+            tooltip="Select chosen sample",
+            icon='fa-angle-down',
+            layout=self.BUTTON_LAYOUT,
+        )
+
+        self.w_select_all = ipw.Button(
+            description="",
+            button_style='',
+            tooltip="Select all samples",
+            icon='fa-angle-double-down',
+            layout=self.BUTTON_LAYOUT,
+        )
+
+        return ipw.VBox(
+            layout={},
+            children=[
+                self.w_update,
+                self.w_select,
+                self.w_select_all,
+            ],
+        )
+
+    def _build_selected_section(self) -> ipw.VBox:
+        """docstring"""
+
+        w_selected_label = ipw.HTML(
+            value="Selected ID:",
+            layout=self.LABEL_LAYOUT,
+        )
+
+        deselection_controls = self._build_deselection_controls()
+
+        self.w_selected_list = ipw.SelectMultiple(
+            rows=10,
+            style=self.BOX_STYLE,
+            layout=self.BOX_LAYOUT,
+        )
+
+        return ipw.VBox(
+            layout={},
+            children=[
+                ipw.HBox(
+                    layout={},
+                    children=[
+                        ipw.VBox(
+                            layout=self.CONTROLS_LAYOUT,
+                            children=[
+                                w_selected_label,
+                                deselection_controls,
+                            ],
+                        ),
+                        self.w_selected_list,
+                    ],
+                ),
+            ],
+        )
+
+    def _build_deselection_controls(self) -> ipw.VBox:
+        """docstring"""
+
+        self.w_deselect = ipw.Button(
+            description="",
+            button_style='',
+            tooltip="Deselect chosen sample",
+            icon='fa-angle-up',
+            layout=self.BUTTON_LAYOUT,
+        )
+
+        self.w_deselect_all = ipw.Button(
+            description="",
+            button_style='',
+            tooltip="Deselect all samples",
+            icon='fa-angle-double-up',
+            layout=self.BUTTON_LAYOUT,
+        )
+
+        return ipw.VBox(
+            layout={},
+            children=[
+                self.w_deselect_all,
+                self.w_deselect,
+            ],
+        )
+
+    ###########################
+    # TODO migrate to presenter
+    ###########################
+
+    def update_protocol_options(self) -> None:
+        """docstring"""
+        self.on_deselect_all_button_click()
+        self.experiment_model.update_available_protocols()
+        self._build_protocol_options()
+
+    def on_update_button_click(self, _=None) -> None:
+        """docstring"""
+        self.update_protocol_options()
+
+    def on_select_list_click(self, change: dict) -> None:
+        """docstring"""
+        self.reset_selection_details()
+        self.add_selection_detail_tabs(change["new"])
+
+    def on_select_button_click(self, _=None) -> None:
+        """docstring"""
+        if indices := self.w_protocol_list.value:
+            self.experiment_model.add_selected_protocols(indices)
+        self.update_selected_list_options()
+
+    def on_select_all_button_click(self, _=None) -> None:
+        """docstring"""
+        if indices := get_ids(self.w_protocol_list.options):
+            self.experiment_model.add_selected_protocols(indices)
+        self.update_selected_list_options()
+
+    def on_selected_list_change(self, _=None) -> None:
+        """docstring"""
+        self.update_validate_button_state()
+
+    def on_deselect_button_click(self, _=None) -> None:
+        """docstring"""
+        if indices := self.w_selected_list.value:
+            self.experiment_model.remove_selected_protocols(indices)
+        self.update_selected_list_options()
+
+    def on_deselect_all_button_click(self, _=None) -> None:
+        """docstring"""
+        if indices := get_ids(self.w_selected_list.options):
+            self.experiment_model.remove_selected_protocols(indices)
+        self.update_selected_list_options()
+
+    def on_validate_button_click(self, callback_function: Callable):
+        """docstring"""
+        return callback_function(self)
+
+    def update_validate_button_state(self) -> None:
+        """docstring"""
+        self.w_validate.disabled = not self.w_selected_list.options
+
+    def update_selected_list_options(self) -> None:
+        """docstring"""
+        selected_protocols = self.experiment_model.selected_protocols.items()
+        options = [(p.name, i) for i, p in selected_protocols]
+        self.w_selected_list.options = options
+
+    def reset_selection_details(self) -> None:
+        """docstring"""
+        self.selection_details.children = []
+        self.selection_details.selected_index = None
+
+    def add_selection_detail_tabs(self, indices: List[int]) -> None:
+        """docstring"""
+
+        if not indices:
+            return
+
+        protocols = self.experiment_model.query_available_protocols(indices)
+
+        for protocol in protocols:
+
+            output = ipw.Output()
+
+            self.selection_details.children += (output, )
+            index = len(self.selection_details.children) - 1
+            self.selection_details.set_title(index, protocol.name)
+
+            self.display_protocol_details(output, protocol)
+
+        self.selection_details.selected_index = 0
+
+    def display_protocol_details(
+        self,
+        output: ipw.Output,
+        protocol: ElectroChemPayloads,
+    ) -> None:
+        """docstring"""
+        with output:
+            for step in protocol.method:
+                print(f"{step.name} ({step.technique})")
+                for label, param in step.parameters:
+                    default = param.default_value
+                    value = default if param.value is None else param.value
+                    units = "" if value is None else param.units
+                    print(f"{label} = {value} {units}")
+                print()
+
+    def reset(self, _=None) -> None:
+        """docstring"""
+        self.w_protocol_list.value = []
+        self.w_selected_list.options = []
+        self.experiment_model.reset_selected_protocols()
+
+    def _build_protocol_options(self) -> None:
+        """docstring"""
+        available_protocols = self.experiment_model.query_available_protocols()
+        options = [(p.name, i) for i, p in enumerate(available_protocols)]
+        self.w_protocol_list.options = options
+
+    def _initialize_selectors(self) -> None:
+        """docstring"""
+        self.w_protocol_list.value = []
+        self.w_selected_list.value = []
+        self.on_update_button_click()
+
+    def _set_event_listeners(self, validate_callback_f) -> None:
+        """docstring"""
+
+        self.w_update.on_click(self.on_update_button_click)
+        self.w_select.on_click(self.on_select_button_click)
+        self.w_select_all.on_click(self.on_select_all_button_click)
+        self.w_deselect.on_click(self.on_deselect_button_click)
+        self.w_deselect_all.on_click(self.on_deselect_all_button_click)
+
+        self.w_protocol_list.observe(
+            names="value",
+            handler=self.on_select_list_click,
+        )
+
+        self.w_selected_list.observe(
+            names='options',
+            handler=self.on_selected_list_change,
+        )
+
+        self.w_validate.on_click(
+            lambda arg: self.on_validate_button_click(validate_callback_f))
+
+        self.reset_button.on_click(self.reset)
+
+
+def get_ids(options: Tuple[Tuple[str, int], ...]) -> List[int]:
+    """Extract indices from option tuples.
+
+    Parameters
+    ----------
+    options : `Tuple[Tuple[str, int], ...]`
+        A tuple of `ipywidgets.SelectMultiple` option tuples.
+
+    Returns
+    -------
+    `List[int]`
+        A list of option indices.
+    """
+    return [i for _, i in options]

From 9f65f6368c9e8cfabccd2c5df703cfe6b089097a Mon Sep 17 00:00:00 2001
From: Edan Bainglass <edan.bainglass@gmail.com>
Date: Mon, 4 Sep 2023 05:49:03 +0000
Subject: [PATCH 2/8] Connect protocol selector to experiment builder

---
 aurora/experiment/submit_experiment.py | 48 +++++++++++---------------
 1 file changed, 21 insertions(+), 27 deletions(-)

diff --git a/aurora/experiment/submit_experiment.py b/aurora/experiment/submit_experiment.py
index 5b7670be..52f43b95 100644
--- a/aurora/experiment/submit_experiment.py
+++ b/aurora/experiment/submit_experiment.py
@@ -8,7 +8,7 @@
 from aurora.common.models import AvailableSamplesModel, BatteryExperimentModel
 from aurora.engine import submit_experiment
 
-from .protocols import CyclingCustom, CyclingStandard
+from .protocols import CyclingCustom, ProtocolSelector
 from .samples import SampleFromId, SampleFromRecipe, SampleFromSpecs
 from .tomato import TomatoSettings
 
@@ -39,9 +39,9 @@ class ExperimentBuilder(ipw.VBox):
         'recipe',
     ]
 
-    _METHOD_LABELS = [
-        'Standardized',
-        'Customized',
+    _PROTOCOL_TAB_LABELS = [
+        'Select',
+        'Create',
     ]
 
     _SAMPLE_BOX_LAYOUT = {
@@ -131,32 +131,26 @@ def _build_sample_selection_section(self) -> None:
     def _build_cycling_protocol_section(self) -> None:
         """Build the cycling protocol section."""
 
-        self.w_test_sample_label = ipw.HTML("Selected samples:")
-        self.w_test_sample_preview = ipw.Output(layout=self._SAMPLE_BOX_LAYOUT)
-
-        self.w_test_standard = CyclingStandard(lambda x: x)
+        self.protocol_selector = ProtocolSelector(
+            experiment_model=self.experiment_model,
+            validate_callback_f=self.confirm_protocols_selection,
+        )
 
-        self.w_test_custom = CyclingCustom(
+        self.protocol_creator = CyclingCustom(
             experiment_model=self.experiment_model,
             validate_callback_f=self.return_selected_protocol,
         )
 
-        self.w_test_method_tab = ipw.Tab(
+        self.w_protocols_tab = ipw.Tab(
             children=[
-                self.w_test_standard,
-                self.w_test_custom,
+                self.protocol_selector,
+                self.protocol_creator,
             ],
-            selected_index=1,
+            selected_index=0,
         )
 
-        for i, title in enumerate(self._METHOD_LABELS):
-            self.w_test_method_tab.set_title(i, title)
-
-        self.w_test_tab = ipw.VBox([
-            self.w_test_sample_label,
-            self.w_test_sample_preview,
-            self.w_test_method_tab,
-        ])
+        for i, title in enumerate(self._PROTOCOL_TAB_LABELS):
+            self.w_protocols_tab.set_title(i, title)
 
     def _build_job_settings_section(self) -> None:
         """Build the job settings section."""
@@ -278,9 +272,9 @@ def selected_recipe(self):
         return self._selected_battery_recipe
 
     @property
-    def selected_cycling_protocol(self):
+    def selected_cycling_protocols(self):
         "The Cycling Specs selected. Used by a BatteryCyclerExperiment."
-        return self.experiment_model.selected_protocol
+        return self.experiment_model.selected_protocols.values()
         # return self._selected_cycling_protocol
 
     @property
@@ -338,11 +332,9 @@ def return_selected_protocol(self, cycling_widget_obj):
         self._selected_cycling_protocol = cycling_widget_obj.protocol_steps_list
         self.post_protocol_selection()
 
-    def post_protocol_selection(self):
+    def confirm_protocols_selection(self, _=None):
         "Switch to Tomato settings accordion tab."
-        if self.selected_battery_samples is None:
-            raise ValueError("A Battery sample was not selected!")
-        # self.w_settings_tab.set_default_calcjob_node_label(self.selected_battery_sample_node.label, self.selected_cycling_protocol_node.label)  # TODO: uncomment this
+        self.w_settings_tab.update_protocol_options()
         self.w_main_accordion.selected_index = 2
 
     #######################################################################################
@@ -414,6 +406,7 @@ def presubmission_checks_preview(self, _=None) -> None:
     @w_submission_output.capture()
     def submit_job(self, dummy=None):
         self.w_submit_button.disabled = True
+
         for index, battery_sample in self.experiment_model.selected_samples.iterrows(
         ):
             json_stuff = dict_to_formatted_json(battery_sample)
@@ -485,6 +478,7 @@ def reset(self, dummy=None):
         # TODO: properly reinitialize each widget
         self.reset_all_inputs()
         self.w_sample_from_id.reset()
+        self.protocol_selector.reset()
         self.w_settings_tab.reset()
         self.w_submission_output.clear_output()
         self.w_main_accordion.selected_index = 0

From f23d7c873b70b01558b5dae7b3c1efa0d8e528e7 Mon Sep 17 00:00:00 2001
From: Edan Bainglass <edan.bainglass@gmail.com>
Date: Mon, 4 Sep 2023 05:55:16 +0000
Subject: [PATCH 3/8] Update settings widget for multiple protocols

---
 aurora/experiment/submit_experiment.py |  52 +++++-----
 aurora/experiment/tomato/settings.py   | 128 ++++++++++++++++++++++---
 2 files changed, 146 insertions(+), 34 deletions(-)

diff --git a/aurora/experiment/submit_experiment.py b/aurora/experiment/submit_experiment.py
index 52f43b95..c2236831 100644
--- a/aurora/experiment/submit_experiment.py
+++ b/aurora/experiment/submit_experiment.py
@@ -1,8 +1,10 @@
 import json
-from typing import Optional
+from copy import deepcopy
+from typing import Dict, Optional
 
 import ipywidgets as ipw
 from aiida_aurora.schemas.battery import BatterySample
+from aiida_aurora.schemas.dgbowl import Tomato_0p2
 from aiida_aurora.schemas.utils import dict_to_formatted_json
 
 from aurora.common.models import AvailableSamplesModel, BatteryExperimentModel
@@ -155,7 +157,9 @@ def _build_cycling_protocol_section(self) -> None:
     def _build_job_settings_section(self) -> None:
         """Build the job settings section."""
         self.w_settings_tab = TomatoSettings(
-            validate_callback_f=self.return_selected_settings)
+            experiment_model=self.experiment_model,
+            validate_callback_f=self.return_selected_settings,
+        )
 
     def _build_job_submission_section(self) -> None:
         """Build the job submission section."""
@@ -274,23 +278,25 @@ def selected_recipe(self):
     @property
     def selected_cycling_protocols(self):
         "The Cycling Specs selected. Used by a BatteryCyclerExperiment."
-        return self.experiment_model.selected_protocols.values()
+        return list(self.experiment_model.selected_protocols.values())
         # return self._selected_cycling_protocol
 
     @property
-    def selected_tomato_settings(self):
+    def selected_tomato_settings(self) -> Dict[str, Tomato_0p2]:
         "The Tomato Settings selected. Used by a BatteryCyclerExperiment."
-        return self._selected_tomato_settings
+        return deepcopy(self._selected_tomato_settings)
 
     @property
-    def selected_monitor_settings(self):
+    def selected_monitor_settings(self) -> Dict[str, dict]:
         "The Tomato Monitor Settings selected. Used by a job monitor."
-        return self._selected_monitor_settings
+        return deepcopy(self._selected_monitor_settings)
 
     @property
-    def calcjob_node_label(self):
-        "The label assigned the submitted BatteryCyclerExperiment CalcJob."
-        return self._calcjob_node_label
+    def workchain_node_label(self):
+        """The label assigned to the submitted workchain node. The
+        label used in the workflow as a prefix for each submitted
+        protocol calculation node."""
+        return self._workchain_node_label
 
     #######################################################################################
     # SAMPLE SELECTION
@@ -340,11 +346,11 @@ def confirm_protocols_selection(self, _=None):
     #######################################################################################
     # TOMATO SETTINGS SELECTION
     #######################################################################################
-    def return_selected_settings(self, settings_widget_obj):
-        self._selected_tomato_settings = settings_widget_obj.selected_tomato_settings
-        self._selected_monitor_settings = settings_widget_obj.selected_monitor_settings
-        self._calcjob_node_label = settings_widget_obj.calcjob_node_label
-        settings_widget_obj.reset_controls()
+    def return_selected_settings(self, settings_widget: TomatoSettings):
+        self._selected_tomato_settings = deepcopy(settings_widget.settings)
+        self._selected_monitor_settings = deepcopy(settings_widget.monitors)
+        self._workchain_node_label = settings_widget.workchain_node_label
+        settings_widget.reset_controls()
         self.post_settings_selection()
 
     def post_settings_selection(self):
@@ -415,13 +421,13 @@ def submit_job(self, dummy=None):
 
             self.process = submit_experiment(
                 sample=current_battery,
-                method=self.selected_cycling_protocol,
-                tomato_settings=self.selected_tomato_settings,
-                monitor_settings=self.selected_monitor_settings,
+                protocols=self.selected_cycling_protocols,
+                settings=self.selected_tomato_settings.values(),
+                monitors=self.selected_monitor_settings.values(),
                 code_name=self.w_code.value,
                 sample_node_label="",
-                method_node_label="",
-                calcjob_node_label="")
+                protocol_node_label="",
+                workchain_node_label="")
 
         self.w_main_accordion.selected_index = None
 
@@ -469,9 +475,9 @@ def reset_all_inputs(self, dummy=None):
         self._selected_battery_specs = None
         self._selected_recipe = None
         self._selected_cycling_protocol = None
-        self._selected_tomato_settings = None
-        self._selected_monitor_settings = None
-        self._calcjob_node_label = None
+        self._selected_tomato_settings = {}
+        self._selected_monitor_settings = {}
+        self._workchain_node_label = None
 
     def reset(self, dummy=None):
         "Reset the interface."
diff --git a/aurora/experiment/tomato/settings.py b/aurora/experiment/tomato/settings.py
index 52292f7d..c5e1c1a5 100644
--- a/aurora/experiment/tomato/settings.py
+++ b/aurora/experiment/tomato/settings.py
@@ -8,6 +8,8 @@
 from aiida_aurora.schemas.dgbowl import Tomato_0p2
 from aiida_aurora.schemas.utils import remove_empties_from_dict_decorator
 
+from aurora.common.models.battery_experiment import BatteryExperimentModel
+
 
 class TomatoSettings(ipw.VBox):
 
@@ -22,16 +24,42 @@ class TomatoSettings(ipw.VBox):
         'padding': '5px'
     }
 
-    def __init__(self, validate_callback_f):
+    def __init__(
+        self,
+        experiment_model: BatteryExperimentModel,
+        validate_callback_f,
+    ) -> None:
 
         if not callable(validate_callback_f):
             raise TypeError(
                 "validate_callback_f should be a callable function")
 
+        self.experiment_model = experiment_model
+
+        self.settings: Dict[str, Tomato_0p2] = {}
+        self.monitors: Dict[str, dict] = {}
+
         # initialize job settings
 
         self.defaults: Dict[ipw.ValueWidget, Any] = {}
 
+        self.protocol_selector = ipw.Dropdown(
+            layout={},
+            value=None,
+            description="Protocol:",
+        )
+        self.defaults[self.protocol_selector] = self.protocol_selector.value
+
+        self.save_button = ipw.Button(
+            layout=self.BUTTON_LAYOUT,
+            style=self.BUTTON_STYLE,
+            disabled=True,
+            button_style="success",
+            description="Save",
+            tooltip="Assign settings/monitors to selected protocol")
+
+        self.save_notice = ipw.HTML()
+
         self.w_job_header = ipw.HTML("<h2>Tomato Job configuration:</h2>")
 
         self.unlock_when_done = ipw.Checkbox(
@@ -91,9 +119,9 @@ def __init__(self, validate_callback_f):
 
         self.w_monitor_parameters = ipw.VBox()
 
-        self.w_job_calcjob_node_label = ipw.Text(
-            description="AiiDA CalcJob node label:",
-            placeholder="Enter a name for the BatteryCyclerExperiment node",
+        self.w_workchain_node_label = ipw.Text(
+            description="AiiDA WorkChain node label:",
+            placeholder="Enter a name for the CyclingSequenceWorkChain node",
             layout={
                 'width': 'auto',
                 "margin": "5px 0",
@@ -103,6 +131,7 @@ def __init__(self, validate_callback_f):
                                      button_style='success',
                                      tooltip="Validate the settings",
                                      icon='check',
+                                     disabled=True,
                                      style=self.BUTTON_STYLE,
                                      layout=self.BUTTON_LAYOUT)
 
@@ -118,13 +147,23 @@ def __init__(self, validate_callback_f):
         # initialize widgets
         super().__init__()
         self.children = [
+            ipw.HBox(
+                layout={
+                    "align_items": "center",
+                },
+                children=[
+                    self.protocol_selector,
+                    self.save_button,
+                    self.save_notice,
+                ],
+            ),
             self.w_job_header,
             ipw.VBox([self.unlock_when_done, self.verbosity],
                      layout=self.BOX_LAYOUT_2),
             self.w_monitor_header,
             ipw.VBox([self.is_monitored, self.w_monitor_parameters],
                      layout=self.BOX_LAYOUT_2),
-            self.w_job_calcjob_node_label,
+            self.w_workchain_node_label,
             ipw.HBox(
                 layout={
                     "align_items": "center",
@@ -137,13 +176,26 @@ def __init__(self, validate_callback_f):
         ]
 
         # setup automations
+
+        self.protocol_selector.observe(
+            names="value",
+            handler=self.update_save_button_states,
+        )
+
+        self.protocol_selector.observe(
+            names="options",
+            handler=self.update_validate_button_states,
+        )
+
+        self.save_button.on_click(self.save_state_to_protocol)
+
         # job monitored checkbox
         self.is_monitored.observe(self._build_job_monitor_parameters,
                                   names="value")
 
         # validate protocol
         self.w_validate.on_click(
-            lambda arg: self.callback_call(validate_callback_f))
+            lambda arg: self.validate(validate_callback_f))
 
         self.reset_button.on_click(self.reset)
 
@@ -152,6 +204,7 @@ def __init__(self, validate_callback_f):
     def init(self) -> None:
         """Initialize widget."""
         self._build_job_monitor_parameters()
+        self.update_protocol_options()
 
     @property
     @remove_empties_from_dict_decorator
@@ -186,8 +239,37 @@ def selected_tomato_settings(self):
         return Tomato_0p2.parse_obj(self.selected_tomato_settings_dict)
 
     @property
-    def calcjob_node_label(self):
-        return self.w_job_calcjob_node_label.value,
+    def workchain_node_label(self):
+        return self.w_workchain_node_label.value,
+
+    def update_protocol_options(self) -> None:
+        """Rebuild protocol dropdown menu."""
+        self.reset()
+        self._build_protocol_options()
+
+    def update_save_button_states(self, change: dict) -> None:
+        """docstring"""
+        self.save_button.disabled = not change["new"]
+
+    def update_validate_button_states(self, change: dict) -> None:
+        """docstring"""
+        self.w_validate.disabled = not change["new"]
+
+    def save_state_to_protocol(self, _=None) -> None:
+        """Save selected settings/monitors to selected protocol."""
+
+        selected_protocol = self.protocol_selector.value
+
+        self.settings[selected_protocol] = self.selected_tomato_settings
+
+        if self.selected_monitor_settings:
+            self.monitors[selected_protocol] = {
+                "capacity": self.selected_monitor_settings
+            }
+        else:
+            self.monitors[selected_protocol] = {}
+
+        self.save_notice.value = f"Saved to {selected_protocol}!"
 
     def _build_job_monitor_parameters(self, dummy=None):
         if self.is_monitored.value:
@@ -200,18 +282,42 @@ def _build_job_monitor_parameters(self, dummy=None):
         else:
             self.w_monitor_parameters.children = []
 
+    def _build_protocol_options(self) -> None:
+        """Build protocol dropdown menu from selected protocols."""
+        selected_protocols = self.experiment_model.selected_protocols.values()
+        options = [p.name for p in selected_protocols]
+        self.protocol_selector.options = options
+        self.protocol_selector.value = None
+
     def reset_controls(self) -> None:
         """Reset controls and notices."""
+        self.save_notice.value = ""
         for control, value in self.defaults.items():
             control.value = value
 
     def reset(self, _=None) -> None:
         """Reset widget and registers."""
         self.reset_controls()
+        self.settings.clear()
+        self.monitors.clear()
 
     def set_default_calcjob_node_label(self, sample_label, method_label):
-        self.w_job_calcjob_node_label.value = f"{sample_label}-{method_label}"
+        self.w_workchain_node_label.value = f"{sample_label}-{method_label}"
+
+    def validate(self, callback_function):
+        "Finalize data and trigger callback."
+
+        for protocol in self.protocol_selector.options:
+            if protocol not in self.settings:
+                self.select_defaults(protocol)
 
-    def callback_call(self, callback_function):
-        "Call a callback function and this class instance to it."
         return callback_function(self)
+
+    def select_defaults(self, protocol: str) -> None:
+        """docstring"""
+        self.settings[protocol] = Tomato_0p2.parse_obj(
+            obj={
+                'unlock_when_done': self.defaults[self.unlock_when_done],
+                'verbosity': self.defaults[self.verbosity],
+            })
+        self.monitors[protocol] = {}

From c6d80fc5aa3ac2b614aecd52cc6ee952621fe9dd Mon Sep 17 00:00:00 2001
From: Edan Bainglass <edan.bainglass@gmail.com>
Date: Mon, 4 Sep 2023 13:12:00 +0000
Subject: [PATCH 4/8] Update submit function for workflow

---
 INSTALLATION_GUIDE.md                  |   3 +-
 aurora/engine/submit.py                | 187 ++++++++++++++++++-------
 aurora/experiment/submit_experiment.py |   4 +-
 3 files changed, 139 insertions(+), 55 deletions(-)

diff --git a/INSTALLATION_GUIDE.md b/INSTALLATION_GUIDE.md
index d2a7fdd6..a47b6b18 100644
--- a/INSTALLATION_GUIDE.md
+++ b/INSTALLATION_GUIDE.md
@@ -234,8 +234,7 @@
   ```
   verdi group create BatterySamples
   verdi group create CyclingSpecs
-  verdi group create CalcJobs
-  verdi group create MonitorJobs
+  verdi group create WorkChains
   ```
 
 ## 4. Aurora app installation
diff --git a/aurora/engine/submit.py b/aurora/engine/submit.py
index 6ebfd07e..b2236393 100644
--- a/aurora/engine/submit.py
+++ b/aurora/engine/submit.py
@@ -1,82 +1,167 @@
-# from time import sleep
+from typing import Dict, List
 
-import aiida
 from aiida.engine import submit
 from aiida.manage.configuration import load_profile
-from aiida.orm import Dict, load_code, load_group
+from aiida.orm import Dict as AiiDADict
+from aiida.orm import List as AiiDAList
+from aiida.orm import load_code, load_group
+from aiida_aurora.data import (BatterySampleData, CyclingSpecsData,
+                               TomatoSettingsData)
+from aiida_aurora.schemas.battery import BatterySample
+from aiida_aurora.schemas.cycling import ElectroChemSequence
+from aiida_aurora.schemas.dgbowl import Tomato_0p2
+from aiida_aurora.workflows import CyclingSequenceWorkChain
 
 load_profile()
 
-BatterySampleData = aiida.plugins.DataFactory('aurora.batterysample')
-CyclingSpecsData = aiida.plugins.DataFactory('aurora.cyclingspecs')
-TomatoSettingsData = aiida.plugins.DataFactory('aurora.tomatosettings')
-BatteryCyclerExperiment = aiida.plugins.CalculationFactory('aurora.cycler')
+SAMPLES_GROUP = load_group("BatterySamples")
+PROTOCOLS_GROUP = load_group("CyclingSpecs")
+WORKFLOWS_GROUP = load_group("WorkChains")
 
-GROUP_SAMPLES = load_group("BatterySamples")
-GROUP_METHODS = load_group("CyclingSpecs")
-GROUP_CALCJOBS = load_group("CalcJobs")
 
-
-def submit_experiment(sample,
-                      method,
-                      tomato_settings,
-                      monitor_settings,
-                      code_name,
-                      sample_node_label="",
-                      method_node_label="",
-                      calcjob_node_label=""):
+def submit_experiment(
+    sample: BatterySample,
+    protocols: List[ElectroChemSequence],
+    settings: List[Tomato_0p2],
+    monitors: List[dict],
+    code_name: str,
+    sample_node_label="",
+    protocol_node_label="",
+    workchain_node_label="",
+) -> CyclingSequenceWorkChain:
     """
     sample : `aiida_aurora.schemas.battery.BatterySample`
     method : `aiida_aurora.schemas.cycling.ElectroChemSequence`
     tomato_settings : `aiida_aurora.schemas.dgbowl_schemas.Tomato_0p2`
     """
 
+    inputs = get_inputs(
+        sample,
+        sample_node_label,
+        code_name,
+        protocols,
+        settings,
+        monitors,
+        protocol_node_label,
+    )
+
+    return submit_job(inputs, workchain_node_label)
+
+
+def get_inputs(
+    sample: BatterySample,
+    sample_node_label: str,
+    code_name: str,
+    protocols: List[ElectroChemSequence],
+    settings: List[Tomato_0p2],
+    monitors: List[dict],
+    protocol_node_label: str,
+) -> dict:
+    """Prepare input dictionaries for workflow."""
+
+    inputs = {
+        "battery_sample": build_sample_node(sample, sample_node_label),
+        "tomato_code": load_code(code_name),
+        "protocol_order": AiiDAList(),
+        "protocols": {},
+        "control_settings": {},
+        "monitor_settings": {},
+    }
+
+    # push cycler locking (if requested) to final workflow step
+    if any(not ts.unlock_when_done for ts in settings):
+        for ts in settings:
+            ts.unlock_when_done = True
+        settings[-1].unlock_when_done = False
+
+    for protocol, settings, protocol_monitors in zip(
+            protocols,
+            settings,
+            monitors,
+    ):
+
+        step = protocol.name
+
+        inputs["protocol_order"].append(step)
+
+        inputs["protocols"][step] = build_protocol_node(
+            protocol,
+            protocol_node_label,
+        )
+
+        inputs["control_settings"][step] = build_settings_node(settings)
+
+        inputs["monitor_settings"][step] = build_monitors_input(
+            protocol,
+            protocol_monitors,
+        )
+
+    return inputs
+
+
+def build_sample_node(
+    sample: BatterySample,
+    sample_node_label: str,
+) -> BatterySampleData:
+    """Construct an AiiDA data node from battery sample data."""
     sample_node = BatterySampleData(sample.dict())
-    if sample_node_label:
-        sample_node.label = sample_node_label
+    sample_node.label = sample_node_label
     sample_node.store()
-    GROUP_SAMPLES.add_nodes(sample_node)
+    SAMPLES_GROUP.add_nodes(sample_node)
+    return sample_node
+
+
+def build_protocol_node(
+    protocol: ElectroChemSequence,
+    protocol_node_label: str,
+) -> CyclingSpecsData:
+    """Construct an AiiDA data node from cycling protocol data."""
+    protocol_node = CyclingSpecsData(protocol.dict())
+    protocol_node.label = protocol_node_label
+    protocol_node.store()
+    PROTOCOLS_GROUP.add_nodes(protocol_node)
+    return protocol_node
+
 
-    method_node = CyclingSpecsData(method.dict())
-    if method_node_label:
-        method_node.label = method_node_label
-    method_node.store()
-    GROUP_METHODS.add_nodes(method_node)
+def build_settings_node(settings: Tomato_0p2) -> TomatoSettingsData:
+    """Construct an AiiDA data node from tomato settings data."""
+    settings_node = TomatoSettingsData(settings.dict())
+    settings_node.label = ""
+    settings_node.store()
+    return settings_node
 
-    tomato_settings_node = TomatoSettingsData(tomato_settings.dict())
-    tomato_settings_node.label = ""  # TODO? write default name generator - e.g. "tomato-True-monitor_600"
-    tomato_settings_node.store()
 
-    code = load_code(code_name)
+def build_monitors_input(
+    protocol: ElectroChemSequence,
+    protocol_monitors: Dict[str, dict],
+) -> dict:
+    """Construct a dictionary of `Dict` monitors for the protocol."""
 
-    builder = BatteryCyclerExperiment.get_builder()
-    builder.battery_sample = sample_node
-    builder.code = code
-    builder.protocol = method_node
-    builder.control_settings = tomato_settings_node
+    monitors: Dict[str, dict] = {}
 
-    if monitor_settings:
+    for label, monitor_settings in protocol_monitors.items():
         refresh_rate = monitor_settings.pop("refresh_rate", 600)
-        builder.monitors = {
-            "capacity":
-            Dict({
+        monitor_name = f"{protocol.name}_{label}"
+        monitors[monitor_name] = AiiDADict(
+            dict={
                 "entry_point": "aurora.monitors.capacity_threshold",
                 "minimum_poll_interval": refresh_rate,
                 "kwargs": {
                     "settings": monitor_settings,
                     "filename": "snapshot.json",
                 },
-            }),
-        }
+            })
 
-    job = submit(builder)
-    job.label = calcjob_node_label
-    print(f"Job <{job.pk}> submitted to AiiDA...")
-    GROUP_CALCJOBS.add_nodes(job)
+    return monitors
 
-    if monitor_settings:
-        job.set_extra('monitored', True)
-    else:
-        job.set_extra('monitored', False)
 
-    return job
+def submit_job(
+    inputs: dict,
+    workchain_node_label: str,
+) -> CyclingSequenceWorkChain:
+    """docstring"""
+    workchain = submit(CyclingSequenceWorkChain, **inputs)
+    workchain.label = workchain_node_label
+    print(f"Workflow <{workchain.pk}> submitted to AiiDA...")
+    WORKFLOWS_GROUP.add_nodes(workchain)
+    return workchain
diff --git a/aurora/experiment/submit_experiment.py b/aurora/experiment/submit_experiment.py
index c2236831..f551e784 100644
--- a/aurora/experiment/submit_experiment.py
+++ b/aurora/experiment/submit_experiment.py
@@ -422,8 +422,8 @@ def submit_job(self, dummy=None):
             self.process = submit_experiment(
                 sample=current_battery,
                 protocols=self.selected_cycling_protocols,
-                settings=self.selected_tomato_settings.values(),
-                monitors=self.selected_monitor_settings.values(),
+                settings=list(self.selected_tomato_settings.values()),
+                monitors=list(self.selected_monitor_settings.values()),
                 code_name=self.w_code.value,
                 sample_node_label="",
                 protocol_node_label="",

From d318d9aeaa2b73a2b63b222690bc72950f6a5b3a Mon Sep 17 00:00:00 2001
From: Edan Bainglass <edan.bainglass@gmail.com>
Date: Mon, 4 Sep 2023 15:53:40 +0000
Subject: [PATCH 5/8] Improve widget reset functionality

---
 aurora/common/models/battery_experiment.py | 4 ++--
 aurora/experiment/submit_experiment.py     | 7 ++-----
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/aurora/common/models/battery_experiment.py b/aurora/common/models/battery_experiment.py
index 25aa6ab6..f9f18daa 100644
--- a/aurora/common/models/battery_experiment.py
+++ b/aurora/common/models/battery_experiment.py
@@ -47,8 +47,8 @@ def __init__(self):
 
     def reset_inputs(self):
         """Resets all inputs."""
-        # Not implemented yet...
-        return None
+        self.reset_selected_samples()
+        self.reset_selected_protocols()
 
     # ----------------------------------------------------------------------#
     # METHODS RELATED TO OBSERVABLES
diff --git a/aurora/experiment/submit_experiment.py b/aurora/experiment/submit_experiment.py
index f551e784..dbad8a2e 100644
--- a/aurora/experiment/submit_experiment.py
+++ b/aurora/experiment/submit_experiment.py
@@ -470,10 +470,7 @@ def reset_sample_selection(self, dummy=None):
 
     def reset_all_inputs(self, dummy=None):
         "Reset all the selected inputs."
-        self.experiment_model.reset_inputs()
-        self._selected_battery_samples = None
-        self._selected_battery_specs = None
-        self._selected_recipe = None
+        self.reset_sample_selection()
         self._selected_cycling_protocol = None
         self._selected_tomato_settings = {}
         self._selected_monitor_settings = {}
@@ -487,4 +484,4 @@ def reset(self, dummy=None):
         self.protocol_selector.reset()
         self.w_settings_tab.reset()
         self.w_submission_output.clear_output()
-        self.w_main_accordion.selected_index = 0
+        self.w_main_accordion.selected_index = None

From 66d6e92b26d2e9459e331be9d30c8471473e0033 Mon Sep 17 00:00:00 2001
From: Edan Bainglass <edan.bainglass@gmail.com>
Date: Mon, 4 Sep 2023 15:58:47 +0000
Subject: [PATCH 6/8] Update protocol creation widget

---
 aurora/experiment/protocols/custom.py  | 147 ++++++++++++++-----------
 aurora/experiment/submit_experiment.py |  30 ++++-
 2 files changed, 109 insertions(+), 68 deletions(-)

diff --git a/aurora/experiment/protocols/custom.py b/aurora/experiment/protocols/custom.py
index bd7978c5..8f6dd094 100644
--- a/aurora/experiment/protocols/custom.py
+++ b/aurora/experiment/protocols/custom.py
@@ -3,13 +3,11 @@
 TODO: Enable the user to save a customized protocol.
 """
 import logging
-import os
 from typing import get_args
 
 import aiida_aurora.schemas.cycling
 import ipywidgets as ipw
 from aiida_aurora.schemas.cycling import ElectroChemPayloads
-from ipyfilechooser import FileChooser
 
 from .technique_widget import TechniqueParametersWidget
 
@@ -21,7 +19,9 @@ class CyclingCustom(ipw.VBox):
     BOX_LAYOUT = {'width': '95%'}
     BOX_LAYOUT_3 = {'width': '95%', 'padding': '5px', 'margin': '10px'}
     BUTTON_STYLE = {'description_width': '30%'}
-    BUTTON_LAYOUT = {'margin': '5px'}
+    BUTTON_LAYOUT = {'margin': '5px', 'width': '40%'}
+    SAVE_BUTTON_STYLE = {'description_width': '30%'}
+    SAVE_BUTTON_LAYOUT = {'margin': '5px', 'width': '135px'}
     BUTTON_LAYOUT_2 = {'width': '20%', 'margin': '5px'}
     # BUTTON_LAYOUT_3 = {'width': '43.5%', 'margin': '5px'}
     BUTTON_LAYOUT_3 = {'width': '10%', 'margin': '5px'}
@@ -45,11 +45,45 @@ def __init__(self, experiment_model, validate_callback_f):
 
         # initialize widgets
         self.w_header = ipw.HTML(value="<h2>Custom Protocol</h2>")
-        self.w_protocol_label = ipw.HTML(value="Sequence:")
-        self.w_protocol_steps_list = ipw.Select(rows=10,
-                                                value=None,
-                                                description="",
-                                                layout={})
+
+        self.protocol_name_label = ipw.HTML(value="Protocol name:")
+
+        self.protocol_name = ipw.Text(
+            layout={
+                "width": "auto",
+                "margin": "0 2px",
+            },
+            placeholder="Enter protocol name",
+        )
+
+        self.protocol_name_warning = ipw.Output()
+
+        self.protocol_node_name_label = ipw.HTML(
+            value="Protocol node label (optional):")
+
+        self.protocol_node_name = ipw.Text(
+            placeholder="Enter a name for the CyclingSpecsData node",
+            layout={
+                "width": "auto",
+                "margin": "0 2px",
+            },
+            style=self.BOX_STYLE_2,
+        )
+
+        self.w_protocol_sequence_label = ipw.HTML(value="Sequence:")
+
+        self.w_protocol_steps_list = ipw.Select(
+            layout={
+                "width": "auto",
+                "margin": "0 2px",
+            },
+            rows=10,
+            value=None,
+            description="",
+        )
+
+        self.w_selected_step_params_action_info = ipw.HTML()
+        self.w_save_info = ipw.HTML()
 
         self._update_protocol_steps_list_widget_options()
 
@@ -78,29 +112,13 @@ def __init__(self, experiment_model, validate_callback_f):
                                         style=self.BUTTON_STYLE,
                                         layout=self.BUTTON_LAYOUT_2)
 
-        self.w_button_load = ipw.Button(description="Load",
-                                        button_style='',
-                                        tooltip="Load protocol",
-                                        icon='',
-                                        style=self.BUTTON_STYLE,
-                                        layout=self.BUTTON_LAYOUT_3)
         self.w_button_save = ipw.Button(description="Save",
-                                        button_style='',
+                                        button_style='success',
                                         tooltip="Save protocol",
                                         icon='',
-                                        style=self.BUTTON_STYLE,
-                                        layout=self.BUTTON_LAYOUT_3)
-        home_directory = os.path.expanduser('~')
-        self.w_filepath_explorer = FileChooser(
-            home_directory,
-            layout={
-                "flex": "1",
-                'margin': '5px'
-            },
-        )
-        self.w_filepath_explorer.default_path = home_directory
-        self.w_filepath_explorer.default_filename = 'saved_protocol.json'
-        self.w_filepath_explorer.reset()
+                                        disabled=True,
+                                        style=self.SAVE_BUTTON_STYLE,
+                                        layout=self.SAVE_BUTTON_LAYOUT)
 
         # initialize protocol steps list
         # self._protocol_steps_list = ElectroChemSequence(method=[])
@@ -130,37 +148,10 @@ def __init__(self, experiment_model, validate_callback_f):
             style=self.BUTTON_STYLE,
             layout=self.BUTTON_LAYOUT_2)
 
-        self.w_method_node_label = ipw.Text(
-            description="AiiDA Method node label:",
-            placeholder="Enter a name for the CyclingSpecsData node",
-            layout={
-                'width': 'auto',
-                "margin": "5px 0",
-            },
-            style=self.BOX_STYLE_2,
-        )
-
-        self.w_validate = ipw.Button(description="Validate",
-                                     button_style='success',
-                                     tooltip="Validate the selected test",
-                                     icon='check',
-                                     disabled=False,
-                                     style=self.BUTTON_STYLE,
-                                     layout=self.BUTTON_LAYOUT)
-
         # initialize widgets
         super().__init__()
         self.children = [
             self.w_header,
-            ipw.HBox(
-                layout={},
-                children=[
-                    self.w_filepath_explorer,
-                    self.w_button_load,
-                    self.w_button_save,
-                ],
-            ),
-            self.w_protocol_label,
             ipw.HBox(
                 layout={
                     'width': 'auto',
@@ -172,6 +163,11 @@ def __init__(self, experiment_model, validate_callback_f):
                             "margin": "0 5px 0 0",
                         },
                         children=[
+                            self.protocol_name_label, self.protocol_name,
+                            self.protocol_name_warning,
+                            self.protocol_node_name_label,
+                            self.protocol_node_name,
+                            self.w_protocol_sequence_label,
                             self.w_protocol_steps_list,
                             ipw.HBox(
                                 layout={"justify_content": "space-between"},
@@ -182,6 +178,13 @@ def __init__(self, experiment_model, validate_callback_f):
                                     self.w_button_down,
                                 ],
                             ),
+                            ipw.HBox(
+                                layout={"align_items": "center"},
+                                children=[
+                                    self.w_button_save,
+                                    self.w_save_info,
+                                ],
+                            )
                         ],
                     ),
                     ipw.VBox(
@@ -194,21 +197,26 @@ def __init__(self, experiment_model, validate_callback_f):
                             self.w_selected_step_technique_name,
                             self.w_selected_step_parameters,
                             ipw.HBox(
-                                layout={},
+                                layout={"align_items": "center"},
                                 children=[
                                     self.w_selected_step_params_save_button,
                                     self.w_selected_step_params_discard_button,
+                                    self.w_selected_step_params_action_info,
                                 ],
                             ),
                         ],
                     )
                 ],
             ),
-            self.w_method_node_label,
-            self.w_validate,
         ]
 
         # setup automations
+
+        self.protocol_name.observe(
+            names='value',
+            handler=self.on_protocol_name_change,
+        )
+
         # steps list
         self.w_protocol_steps_list.observe(
             self._build_current_step_properties_widget, names='index')
@@ -223,9 +231,6 @@ def __init__(self, experiment_model, validate_callback_f):
         self.w_button_up.on_click(self.w_button_up_click)
         self.w_button_down.on_click(self.w_button_down_click)
 
-        self.w_button_load.on_click(self.button_load_protocol_click)
-        self.w_button_save.on_click(self.button_save_protocol_click)
-
         # current step's properties:
         #   if technique type changes, we need to initialize a new technique from scratch the widget observer may detect a change
         #   even when a new step is selected therefore we check whether the new technique is the same as the one stored in
@@ -237,10 +242,16 @@ def __init__(self, experiment_model, validate_callback_f):
             self.save_current_step_properties)
         self.w_selected_step_params_discard_button.on_click(
             self.discard_current_step_properties)
-        # validate protocol
-        self.w_validate.on_click(
+
+        # save protocol
+        self.w_button_save.on_click(
             lambda arg: self.callback_call(validate_callback_f))
 
+    def on_protocol_name_change(self, change: dict) -> None:
+        """docstring"""
+        self.w_button_save.disabled = not change["new"]
+        self.reset_info_messages()
+
     def update(self):
         """Receive updates from the model"""
         self._update_protocol_steps_list_widget_options()
@@ -275,6 +286,7 @@ def _count_technique_occurencies(self, technique):
         # return [type(step) for step in self.protocol_steps_list.method].count(technique)
 
     def _update_protocol_steps_list_widget_options(self, new_index=None):
+        self.reset_info_messages()
         old_selected_index = self.w_protocol_steps_list.index
         self.w_protocol_steps_list.options = [
             f"[{idx + 1}] - {step.name}" for idx, step in enumerate(
@@ -338,6 +350,7 @@ def _build_current_step_properties_widget(self, dummy=None):
 
     def _build_technique_parameters_widgets(self, dummy=None):
         """Build widget of parameters for the given technique."""
+        self.reset_info_messages()
         logging.debug("Building technique parameters")
         # check if the technique is the same as the one stored in the selected step
         if isinstance(
@@ -372,12 +385,20 @@ def save_current_step_properties(self, dummy=None):
             f"  Parameters saved: {self.w_selected_step_parameters.selected_tech_parameters.items()}"
         )
         self._update_protocol_steps_list_widget_options()
+        self.w_selected_step_params_action_info.value = "Saved step!"
 
     def discard_current_step_properties(self, dummy=None):
         "Discard parameters of the selected step and reload them from the technique object"
         logging.debug("Discarding current step properties")
         # i.e. just rebuild the parameters widget
         self._build_current_step_properties_widget()
+        self.w_selected_step_params_action_info.value = "Discarded step!"
+
+    def reset_info_messages(self) -> None:
+        """docstring"""
+        self.w_selected_step_params_action_info.value = ""
+        self.w_save_info.value = ""
+        self.protocol_name_warning.clear_output()
 
     def callback_call(self, callback_function):
         "Call a callback function and this class instance to it."
diff --git a/aurora/experiment/submit_experiment.py b/aurora/experiment/submit_experiment.py
index dbad8a2e..2e633750 100644
--- a/aurora/experiment/submit_experiment.py
+++ b/aurora/experiment/submit_experiment.py
@@ -1,4 +1,5 @@
 import json
+import re
 from copy import deepcopy
 from typing import Dict, Optional
 
@@ -140,7 +141,7 @@ def _build_cycling_protocol_section(self) -> None:
 
         self.protocol_creator = CyclingCustom(
             experiment_model=self.experiment_model,
-            validate_callback_f=self.return_selected_protocol,
+            validate_callback_f=self.save_protocol_and_refresh_selector,
         )
 
         self.w_protocols_tab = ipw.Tab(
@@ -333,10 +334,29 @@ def sample_selection_method(self):
     #######################################################################################
     # METHOD SELECTION
     #######################################################################################
-    def return_selected_protocol(self, cycling_widget_obj):
-        self.experiment_model.selected_protocol = cycling_widget_obj.protocol_steps_list
-        self._selected_cycling_protocol = cycling_widget_obj.protocol_steps_list
-        self.post_protocol_selection()
+    def save_protocol_and_refresh_selector(self, custom: CyclingCustom):
+        custom.reset_info_messages()
+        name: str = custom.protocol_name.value
+
+        # invalid name check
+        if not re.match(r"^[\w_]+$", name):
+            with custom.protocol_name_warning:
+                print("Only alphanumeric characters and underscores allowed")
+            return
+
+        # existing name check
+        available_protocols = self.experiment_model.available_protocols
+        if any(protocol.name == name for protocol in available_protocols):
+            with custom.protocol_name_warning:
+                print("Protocol name already exists.\nPlease choose another.")
+            return
+
+        new_protocol = self.experiment_model.selected_protocol
+        new_protocol.set_name(name)
+        self.experiment_model.save_protocol()
+        custom.w_save_info.value = "Saved!"
+
+        self.protocol_selector.update_protocol_options()
 
     def confirm_protocols_selection(self, _=None):
         "Switch to Tomato settings accordion tab."

From 72044291a6fb0647a0ec198b533dacdaf183ad5f Mon Sep 17 00:00:00 2001
From: Edan Bainglass <edan.bainglass@gmail.com>
Date: Mon, 4 Sep 2023 04:30:46 +0000
Subject: [PATCH 7/8] Ignore local JSON files

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 1386c743..934bbc22 100644
--- a/.gitignore
+++ b/.gitignore
@@ -130,3 +130,4 @@ dmypy.json
 
 # Project-specific
 .aurora-*.ipynb
+*.json

From e81fd14cc96586bec3ac13926e2d3b7f1e7bd000 Mon Sep 17 00:00:00 2001
From: Edan Bainglass <edan.bainglass@gmail.com>
Date: Mon, 4 Sep 2023 16:00:12 +0000
Subject: [PATCH 8/8] Redesign input preview section

---
 aurora/experiment/submit_experiment.py | 334 +++++++++++++++++--------
 1 file changed, 235 insertions(+), 99 deletions(-)

diff --git a/aurora/experiment/submit_experiment.py b/aurora/experiment/submit_experiment.py
index 2e633750..859efe24 100644
--- a/aurora/experiment/submit_experiment.py
+++ b/aurora/experiment/submit_experiment.py
@@ -1,4 +1,3 @@
-import json
 import re
 from copy import deepcopy
 from typing import Dict, Optional
@@ -7,6 +6,7 @@
 from aiida_aurora.schemas.battery import BatterySample
 from aiida_aurora.schemas.dgbowl import Tomato_0p2
 from aiida_aurora.schemas.utils import dict_to_formatted_json
+from IPython.display import display
 
 from aurora.common.models import AvailableSamplesModel, BatteryExperimentModel
 from aurora.engine import submit_experiment
@@ -24,10 +24,10 @@ class ExperimentBuilder(ipw.VBox):
     _SECTION_TITLE = "Submit Experiment"
 
     _ACCORDION_STEPS = [
-        'Sample Selection',
-        'Cycling Protocol',
-        'Job Settings',
-        'Submit Job',
+        'Select samples',
+        'Select protocols',
+        'Configure tomato/monitoring',
+        'Review input',
     ]
 
     _SAMPLE_INPUT_LABELS = [
@@ -55,11 +55,8 @@ class ExperimentBuilder(ipw.VBox):
     }
 
     _SUBMISSION_INPUT_LAYOUT = {
-        'border': 'solid darkgrey 1px',
         'margin': '5px',
         'padding': '5px',
-        'max_height': '500px',
-        'overflow': 'scroll',
     }
 
     _SUBMISSION_OUTPUT_LAYOUT = {
@@ -162,20 +159,71 @@ def _build_job_settings_section(self) -> None:
             validate_callback_f=self.return_selected_settings,
         )
 
-    def _build_job_submission_section(self) -> None:
+    def _build_input_preview_section(self) -> None:
         """Build the job submission section."""
 
-        # TODO: write better preview of the job inputs
-        self.w_job_preview = ipw.Output(layout=self._SUBMISSION_INPUT_LAYOUT)
+        self.input_preview = ipw.Output(layout={"margin": "0 0 10px"})
+
+        self.protocols_preview = ipw.Tab(layout={
+            "min_height": "350px",
+            "max_height": "350px",
+        })
+
+        self.settings_preview = ipw.Output(
+            layout={
+                "flex": "1",
+                "margin": "2px",
+                "border": "solid darkgrey 1px",
+                "overflow_y": "auto",
+            })
+
+        self.monitors_preview = ipw.Output(
+            layout={
+                "flex": "1",
+                "margin": "2px",
+                "border": "solid darkgrey 1px",
+                "overflow_y": "auto",
+            })
+
+        self.valid_input_confirmation = ipw.HTML()
+
+        self.input_preview_section = ipw.VBox(
+            layout={},
+            children=[
+                self.input_preview,
+                self.valid_input_confirmation,
+            ],
+        )
+
+    def _build_accordion(self) -> None:
+        """Combine the sections in the main accordion widget."""
+
+        self.w_main_accordion = ipw.Accordion(
+            layout={},
+            children=[
+                self.w_sample_selection_tab,
+                self.w_protocols_tab,
+                self.w_settings_tab,
+                self.input_preview_section,
+            ],
+            selected_index=None,
+        )
+
+        for i, title in enumerate(self._ACCORDION_STEPS):
+            self.w_main_accordion.set_title(i, title)
+
+    def _build_submission_section(self) -> ipw.HBox:
+        """Build submission controls widgets."""
 
         self.w_code = ipw.Dropdown(
+            layout={},
             description="Select code:",
             options=[CODE_NAME],  # TODO: get codes
             value=CODE_NAME,
         )
 
         self.w_submit_button = ipw.Button(
-            description="SUBMIT",
+            description="Submit",
             button_style="success",
             tooltip="Submit the experiment",
             icon="play",
@@ -184,16 +232,8 @@ def _build_job_submission_section(self) -> None:
             layout=self._BUTTON_LAYOUT,
         )
 
-        self.w_submit_tab = ipw.VBox([
-            self.w_job_preview,
-            self.w_code,
-            self.w_submit_button,
-        ])
-
-    def _build_reset_button(self) -> None:
-        """Build the reset button."""
         self.w_reset_button = ipw.Button(
-            description="RESET",
+            description="Reset",
             button_style="danger",
             tooltip="Start over",
             icon="times",
@@ -201,18 +241,16 @@ def _build_reset_button(self) -> None:
             layout=self._BUTTON_LAYOUT,
         )
 
-    def _build_accordion(self) -> None:
-        """Combine the sections in the main accordion widget."""
-
-        self.w_main_accordion = ipw.Accordion(children=[
-            self.w_sample_selection_tab,
-            self.w_test_tab,
-            self.w_settings_tab,
-            self.w_submit_tab,
-        ])
-
-        for i, title in enumerate(self._ACCORDION_STEPS):
-            self.w_main_accordion.set_title(i, title)
+        self.submission_controls = ipw.HBox(
+            layout={
+                "align_items": "center",
+            },
+            children=[
+                self.w_code,
+                self.w_submit_button,
+                self.w_reset_button,
+            ],
+        )
 
     def _build_widgets(self) -> None:
         """Build panel widgets."""
@@ -223,19 +261,20 @@ def _build_widgets(self) -> None:
 
         self._build_job_settings_section()
 
-        self._build_job_submission_section()
-
-        self._build_reset_button()
+        self._build_input_preview_section()
 
         self._build_accordion()
 
-        super().__init__()
+        self._build_submission_section()
 
-        self.children = [
-            self.w_main_accordion,
-            self.w_reset_button,
-            self.w_submission_output,
-        ]
+        super().__init__(
+            layout={},
+            children=[
+                self.w_main_accordion,
+                self.submission_controls,
+                self.w_submission_output,
+            ],
+        )
 
     def _subscribe_observables(self) -> None:
         """Set up observables."""
@@ -246,6 +285,11 @@ def _subscribe_observables(self) -> None:
             names='selected_index',
         )
 
+        self.protocols_preview.observe(
+            names="selected_index",
+            handler=self.display_settings_and_monitors,
+        )
+
         # trigger presubmission checks when we are in the "Submit Job" accordion tab
         self.w_main_accordion.observe(
             self.presubmission_checks_preview,
@@ -381,6 +425,137 @@ def post_settings_selection(self):
     # SUBMIT JOB
     #######################################################################################
 
+    def display_samples_preview(self) -> None:
+        """docstring"""
+
+        samples = ipw.Output(
+            layout={
+                "max_height": "300px",
+                "overflow_y": "scroll",
+                "align_items": "center",
+            })
+
+        display(
+            ipw.VBox(
+                layout={},
+                children=[
+                    ipw.HTML("<h3 style='margin: 0'>Samples</h3>"),
+                    samples,
+                ],
+            ))
+
+        with samples:
+            self.experiment_model.display_query_results({
+                'battery_id': [
+                    sample.battery_id
+                    for sample in self.selected_battery_samples
+                ]
+            })
+
+    def display_protocols_preview(self) -> None:
+        """docstring"""
+
+        self.protocols_preview.children = []
+        self.protocols_preview.selected_index = None
+
+        self.settings_preview.clear_output()
+        self.monitors_preview.clear_output()
+
+        display(
+            ipw.HBox(
+                layout={
+                    "margin": "0 0 10px",
+                    "grid_gap": "5px",
+                },
+                children=[
+                    ipw.VBox(
+                        layout={
+                            "width": "50%",
+                        },
+                        children=[
+                            ipw.HTML("<h3>Protocols</h3>"),
+                            self.protocols_preview,
+                        ],
+                    ),
+                    ipw.VBox(
+                        layout={
+                            "width": "50%",
+                            "grid_gap": "5px",
+                        },
+                        children=[
+                            ipw.VBox(
+                                layout={
+                                    "flex": "1",
+                                },
+                                children=[
+                                    ipw.HTML("<h3>Settings</h3>"),
+                                    self.settings_preview,
+                                ],
+                            ),
+                            ipw.VBox(
+                                layout={
+                                    "flex": "1",
+                                },
+                                children=[
+                                    ipw.HTML("<h3>Monitors</h3>"),
+                                    self.monitors_preview,
+                                ],
+                            ),
+                        ],
+                    )
+                ],
+            ))
+
+        for protocol in self.selected_cycling_protocols:
+
+            output = ipw.Output()
+
+            self.protocols_preview.children += (output, )
+            index = len(self.protocols_preview.children) - 1
+            self.protocols_preview.set_title(index, protocol.name)
+
+            with output:
+                for step in protocol.method:
+                    print(f"{step.name} ({step.technique})")
+                    for label, param in step.parameters:
+                        default = param.default_value
+                        value = default if param.value is None else param.value
+                        units = "" if value is None else param.units
+                        print(f"{label} = {value} {units}")
+                    print()
+
+        self.protocols_preview.selected_index = 0
+
+    def display_settings_and_monitors(self, change: dict) -> None:
+        """docstring"""
+
+        if (index := change["new"]) is None:
+            return
+
+        protocol = list(self.selected_cycling_protocols)[index]
+        settings = self.selected_tomato_settings.get(protocol.name)
+        monitors = self.selected_monitor_settings.get(protocol.name)
+
+        if settings is None or monitors is None:
+            return
+
+        self.settings_preview.clear_output()
+        with self.settings_preview:
+            for key, value in settings.dict().items():
+                if isinstance(value, dict):
+                    for k, v in value.items():
+                        print(f"{k}: {v}")
+                else:
+                    print(f"{key}: {value}")
+
+        self.monitors_preview.clear_output()
+        with self.monitors_preview:
+            for monitor, monitor_settings in monitors.items():
+                print(f"name: {monitor}")
+                for key, value in monitor_settings.items():
+                    print(f"{key} = {value}")
+            print()
+
     def presubmission_checks_preview(self, _=None) -> None:
         """
         Verify that all the input is there and display preview.
@@ -390,48 +565,36 @@ def presubmission_checks_preview(self, _=None) -> None:
         if self.w_main_accordion.selected_index != 3:
             return
 
-        self.w_job_preview.clear_output()
-
-        with self.w_job_preview:
-
-            if not self._has_valid_settings():
-                return
-
-            output_cycling_protocol = json.dumps(
-                self.selected_cycling_protocol.dict(),
-                indent=2,
-            )
-
-            output_tomato_settings = f'{self.selected_tomato_settings}'
+        self.input_preview.clear_output()
 
-            output_monitor_settings = f'{self.selected_monitor_settings}'
+        with self.input_preview:
 
             if not self.selected_battery_samples:
-                return
+                notice = "No battery samples selected!"
+                return self.signal_missing_input(notice)
 
-            print("Battery Samples:")
+            self.display_samples_preview()
 
-            query = {
-                'battery_id': [
-                    sample.battery_id
-                    for sample in self.selected_battery_samples
-                ]
-            }
-            self.experiment_model.display_query_results(query)
+            if not self.selected_cycling_protocols:
+                notice = "No cycling protocols selected!"
+                return self.signal_missing_input(notice)
 
-            print()
-
-            print(f"Cycling Protocol:\n{output_cycling_protocol}\n")
-            print(f"Tomato Settings:\n{output_tomato_settings}\n")
-            print(f"Monitor Settings:{output_monitor_settings}\n")
+            self.display_protocols_preview()
 
-            print("✅ All good!")
+            if not self.selected_tomato_settings or \
+               not self.selected_monitor_settings:
+                notice = "No protocol settings selected!"
+                return self.signal_missing_input(notice)
 
+        self.valid_input_confirmation.value = "✅ All good!"
         self.w_submit_button.disabled = False
 
+    def signal_missing_input(self, message: str) -> None:
+        """docstring"""
+        self.valid_input_confirmation.value = f"❌ {message}"
+
     @w_submission_output.capture()
     def submit_job(self, dummy=None):
-        self.w_submit_button.disabled = True
 
         for index, battery_sample in self.experiment_model.selected_samples.iterrows(
         ):
@@ -451,33 +614,6 @@ def submit_job(self, dummy=None):
 
         self.w_main_accordion.selected_index = None
 
-    def _has_valid_settings(self) -> bool:
-        """Validate job settings.
-
-        Returns
-        -------
-        `bool`
-            `True` if job settings are valid, `False` otherwise.
-        """
-
-        try:
-
-            if self.selected_battery_samples is None:
-                raise ValueError("A Battery sample was not selected!")
-
-            if self.selected_cycling_protocol is None:
-                raise ValueError("A Cycling protocol was not selected!")
-
-            if self.selected_tomato_settings is None or self.selected_monitor_settings is None:
-                raise ValueError("Tomato settings were not selected!")
-
-            return True
-
-        except ValueError as err:
-            self.w_submit_button.disabled = True
-            print(f"❌ {err}")
-            return False
-
     #######################################################################################
     # RESET
     #######################################################################################