Merge branch 'dev' into bugfix/2676_NMNE_var_access

2024-07-05 14:20:50 +01:00
parent 18ae3acf37 20e5e40d0d
commit 2dcabc9fa7
46 changed files with 2578 additions and 281 deletions
--- a/.azure/azure-benchmark-pipeline.yaml
+++ b/.azure/azure-benchmark-pipeline.yaml
@@ -0,0 +1,84 @@
+trigger:
+  branches:
+    exclude:
+    - '*'
+    include:
+    - 'refs/heads/release/*'
+
+schedules:
+- cron: "0 2 * * 1-5"  # Run at 2 AM every weekday
+  displayName: "Weekday Schedule"
+  branches:
+    include:
+    - 'refs/heads/dev'
+
+pool:
+  vmImage: ubuntu-latest
+
+variables:
+  VERSION: ''
+  MAJOR_VERSION: ''
+
+steps:
+- checkout: self
+  persistCredentials: true
+
+- script: |
+    VERSION=$(cat src/primaite/VERSION | tr -d '\n')
+    if [[ "$(Build.SourceBranch)" == "refs/heads/dev" ]]; then
+      DATE=$(date +%Y%m%d)
+      echo "${VERSION}+dev.${DATE}" > src/primaite/VERSION
+    fi
+  displayName: 'Update VERSION file for Dev Benchmark'
+
+- script: |
+    VERSION=$(cat src/primaite/VERSION | tr -d '\n')
+    MAJOR_VERSION=$(echo $VERSION | cut -d. -f1)
+    echo "##vso[task.setvariable variable=VERSION]$VERSION"
+    echo "##vso[task.setvariable variable=MAJOR_VERSION]$MAJOR_VERSION"
+  displayName: 'Set Version Variables'
+
+- task: UsePythonVersion@0
+  inputs:
+    versionSpec: '3.11'
+    addToPath: true
+
+- script: |
+    python -m pip install --upgrade pip
+    pip install -e .[dev,rl]
+    primaite setup
+  displayName: 'Install Dependencies'
+
+- script: |
+    cd benchmark
+    python3 primaite_benchmark.py
+    cd ..
+  displayName: 'Run Benchmarking Script'
+
+- script: |
+    git config --global user.email "oss@dstl.gov.uk"
+    git config --global user.name "Defence Science and Technology Laboratory UK"
+  workingDirectory: $(System.DefaultWorkingDirectory)
+  displayName: 'Configure Git'
+  condition: and(succeeded(), eq(variables['Build.Reason'], 'Manual'), startsWith(variables['Build.SourceBranch'], 'refs/heads/release'))
+
+- script: |
+    git add benchmark/results/v$(MAJOR_VERSION)/v$(VERSION)/*
+    git commit -m "Automated benchmark output commit for version $(VERSION)"
+    git push origin HEAD:refs/heads/$(Build.SourceBranchName)
+  displayName: 'Commit and Push Benchmark Results'
+  workingDirectory: $(System.DefaultWorkingDirectory)
+  env:
+    GIT_CREDENTIALS: $(System.AccessToken)
+  condition: and(succeeded(), startsWith(variables['Build.SourceBranch'], 'refs/heads/release'))
+
+- script: |
+    tar czf primaite_v$(VERSION)_benchmark.tar.gz benchmark/results/v$(MAJOR_VERSION)/v$(VERSION)
+  displayName: 'Prepare Artifacts for Publishing'
+
+- task: PublishPipelineArtifact@1
+  inputs:
+    targetPath: primaite_v$(VERSION)_benchmark.tar.gz
+    artifactName: 'benchmark-output'
+    publishLocation: 'pipeline'
+  displayName: 'Publish Benchmark Output as Artifact'
--- a/.azure/azure-ci-build-pipeline.yaml
+++ b/.azure/azure-ci-build-pipeline.yaml
@@ -107,11 +107,39 @@ stages:
              coverage html -d htmlcov -i
            displayName: 'Run tests and code coverage'

+          # Run the notebooks
+          - script: |
+              pytest --nbmake -n=auto src/primaite/notebooks --junit-xml=./notebook-tests/notebooks.xml
+              notebooks_exit_code=$?
+              pytest --nbmake -n=auto src/primaite/simulator/_package_data --junit-xml=./notebook-tests/package-notebooks.xml
+              package_notebooks_exit_code=$?
+              # Fail step if either of these do not have exit code 0
+              if [ $notebooks_exit_code -ne 0 ] || [ $package_notebooks_exit_code -ne 0 ]; then
+                exit 1
+              fi
+            displayName: 'Run notebooks on Linux and macOS'
+            condition: or(eq(variables['Agent.OS'], 'Linux'), eq(variables['Agent.OS'], 'Darwin'))
+
+          # Run notebooks
+          - script: |
+              pytest --nbmake -n=auto src/primaite/notebooks --junit-xml=./notebook-tests/notebooks.xml
+              set notebooks_exit_code=%ERRORLEVEL%
+              pytest --nbmake -n=auto src/primaite/simulator/_package_data --junit-xml=./notebook-tests/package-notebooks.xml
+              set package_notebooks_exit_code=%ERRORLEVEL%
+              rem Fail step if either of these do not have exit code 0
+              if %notebooks_exit_code% NEQ 0 exit /b 1
+              if %package_notebooks_exit_code% NEQ 0 exit /b 1
+            displayName: 'Run notebooks on Windows'
+            condition: eq(variables['Agent.OS'], 'Windows_NT')
+
          - task: PublishTestResults@2
            condition: succeededOrFailed()
+            displayName: 'Publish Test Results'
            inputs:
              testRunner: JUnit
-              testResultsFiles: 'junit/**.xml'
+              testResultsFiles: |
+                'junit/**.xml'
+                'notebook-tests/**.xml'
              testRunTitle: 'Publish test results'
              failTaskOnFailedTests: true

--- a/.gitignore
+++ b/.gitignore
@@ -54,6 +54,7 @@ cover/
 tests/assets/**/*.png
 tests/assets/**/tensorboard_logs/
 tests/assets/**/checkpoints/
+notebook-tests/*.xml

 # Translations
 *.mo
--- a/benchmark/primaite_benchmark.py
+++ b/benchmark/primaite_benchmark.py
@@ -117,14 +117,14 @@ class BenchmarkSession:
    def generate_learn_metadata_dict(self) -> Dict[str, Any]:
        """Metadata specific to the learning session."""
        total_s, s_per_step, s_per_100_steps_10_nodes = self._learn_benchmark_durations()
-        self.gym_env.average_reward_per_episode.pop(0)  # remove episode 0
+        self.gym_env.total_reward_per_episode.pop(0)  # remove episode 0
        return {
            "total_episodes": self.gym_env.episode_counter,
            "total_time_steps": self.gym_env.total_time_steps,
            "total_s": total_s,
            "s_per_step": s_per_step,
            "s_per_100_steps_10_nodes": s_per_100_steps_10_nodes,
-            "av_reward_per_episode": self.gym_env.average_reward_per_episode,
+            "total_reward_per_episode": self.gym_env.total_reward_per_episode,
        }


--- a/benchmark/report.py
+++ b/benchmark/report.py
@@ -9,10 +9,6 @@ import plotly.graph_objects as go
 import polars as pl
 import yaml
 from plotly.graph_objs import Figure
-from pylatex import Command, Document
-from pylatex import Figure as LatexFigure
-from pylatex import Section, Subsection, Tabular
-from pylatex.utils import bold
 from utils import _get_system_info

 import primaite
@@ -39,19 +35,19 @@ def _build_benchmark_results_dict(start_datetime: datetime, metadata_dict: Dict,
        "av_s_per_step": sum(d["s_per_step"] for d in metadata_dict.values()) / num_sessions,
        "av_s_per_100_steps_10_nodes": sum(d["s_per_100_steps_10_nodes"] for d in metadata_dict.values())
        / num_sessions,
-        "combined_av_reward_per_episode": {},
-        "session_av_reward_per_episode": {k: v["av_reward_per_episode"] for k, v in metadata_dict.items()},
+        "combined_total_reward_per_episode": {},
+        "session_total_reward_per_episode": {k: v["total_reward_per_episode"] for k, v in metadata_dict.items()},
        "config": config,
    }

    # find the average of each episode across all sessions
-    episodes = metadata_dict[1]["av_reward_per_episode"].keys()
+    episodes = metadata_dict[1]["total_reward_per_episode"].keys()

    for episode in episodes:
        combined_av_reward = (
-            sum(metadata_dict[k]["av_reward_per_episode"][episode] for k in metadata_dict.keys()) / num_sessions
+            sum(metadata_dict[k]["total_reward_per_episode"][episode] for k in metadata_dict.keys()) / num_sessions
        )
-        averaged_data["combined_av_reward_per_episode"][episode] = combined_av_reward
+        averaged_data["combined_total_reward_per_episode"][episode] = combined_av_reward

    return averaged_data

@@ -87,7 +83,7 @@ def _plot_benchmark_metadata(
    fig = go.Figure(layout=layout)
    fig.update_layout(template=PLOT_CONFIG["template"])

-    for session, av_reward_dict in benchmark_metadata_dict["session_av_reward_per_episode"].items():
+    for session, av_reward_dict in benchmark_metadata_dict["session_total_reward_per_episode"].items():
        df = _get_df_from_episode_av_reward_dict(av_reward_dict)
        fig.add_trace(
            go.Scatter(
@@ -100,7 +96,7 @@ def _plot_benchmark_metadata(
            )
        )

-    df = _get_df_from_episode_av_reward_dict(benchmark_metadata_dict["combined_av_reward_per_episode"])
+    df = _get_df_from_episode_av_reward_dict(benchmark_metadata_dict["combined_total_reward_per_episode"])
    fig.add_trace(
        go.Scatter(
            x=df["episode"], y=df["av_reward"], mode="lines", name="Combined Session Av", line={"color": "#FF0000"}
@@ -136,11 +132,11 @@ def _plot_all_benchmarks_combined_session_av(results_directory: Path) -> Figure:

    Does this by iterating over the ``benchmark/results`` directory and
    extracting the benchmark metadata json for each version that has been
-    benchmarked. The combined_av_reward_per_episode is extracted from each,
+    benchmarked. The combined_total_reward_per_episode is extracted from each,
    converted into a polars dataframe, and plotted as a scatter line in plotly.
    """
    major_v = primaite.__version__.split(".")[0]
-    title = f"Learning Benchmarking of All Released Versions under Major v{major_v}.*.*"
+    title = f"Learning Benchmarking of All Released Versions under Major v{major_v}.#.#"
    subtitle = "Rolling Av (Combined Session Av)"
    if title:
        if subtitle:
@@ -162,7 +158,7 @@ def _plot_all_benchmarks_combined_session_av(results_directory: Path) -> Figure:
            metadata_file = dir / f"{dir.name}_benchmark_metadata.json"
            with open(metadata_file, "r") as file:
                metadata_dict = json.load(file)
-            df = _get_df_from_episode_av_reward_dict(metadata_dict["combined_av_reward_per_episode"])
+            df = _get_df_from_episode_av_reward_dict(metadata_dict["combined_total_reward_per_episode"])

            fig.add_trace(go.Scatter(x=df["episode"], y=df["rolling_av_reward"], mode="lines", name=dir.name))

@@ -208,98 +204,77 @@ def build_benchmark_latex_report(

    fig = _plot_all_benchmarks_combined_session_av(results_directory=results_root_path)

-    all_version_plot_path = results_root_path / "PrimAITE Versions Learning Benchmark.png"
+    all_version_plot_path = version_result_dir / "PrimAITE Versions Learning Benchmark.png"
    fig.write_image(all_version_plot_path)

-    geometry_options = {"tmargin": "2.5cm", "rmargin": "2.5cm", "bmargin": "2.5cm", "lmargin": "2.5cm"}
    data = benchmark_metadata_dict
    primaite_version = data["primaite_version"]

-    # Create a new document
-    doc = Document("report", geometry_options=geometry_options)
-    # Title
-    doc.preamble.append(Command("title", f"PrimAITE {primaite_version} Learning Benchmark"))
-    doc.preamble.append(Command("author", "PrimAITE Dev Team"))
-    doc.preamble.append(Command("date", datetime.now().date()))
-    doc.append(Command("maketitle"))
+    with open(version_result_dir / f"PrimAITE v{primaite_version} Learning Benchmark.md", "w") as file:
+        # Title
+        file.write(f"# PrimAITE v{primaite_version} Learning Benchmark\n")
+        file.write("## PrimAITE Dev Team\n")
+        file.write(f"### {datetime.now().date()}\n")
+        file.write("\n---\n")

-    sessions = data["total_sessions"]
-    episodes = session_metadata[1]["total_episodes"] - 1
-    steps = data["config"]["game"]["max_episode_length"]
+        sessions = data["total_sessions"]
+        episodes = session_metadata[1]["total_episodes"] - 1
+        steps = data["config"]["game"]["max_episode_length"]

-    # Body
-    with doc.create(Section("Introduction")):
-        doc.append(
+        # Body
+        file.write("## 1 Introduction\n")
+        file.write(
            f"PrimAITE v{primaite_version} was benchmarked automatically upon release. Learning rate metrics "
-            f"were captured to be referenced during system-level testing and user acceptance testing (UAT)."
+            f"were captured to be referenced during system-level testing and user acceptance testing (UAT).\n"
        )
-        doc.append(
-            f"\nThe benchmarking process consists of running {sessions} training session using the same "
+        file.write(
+            f"The benchmarking process consists of running {sessions} training session using the same "
            f"config file. Each session trains an agent for {episodes} episodes, "
-            f"with each episode consisting of {steps} steps."
+            f"with each episode consisting of {steps} steps.\n"
        )
-        doc.append(
-            f"\nThe total reward per episode from each session is captured. This is then used to calculate an "
+        file.write(
+            f"The total reward per episode from each session is captured. This is then used to calculate an "
            f"caverage total reward per episode from the {sessions} individual sessions for smoothing. "
            f"Finally, a 25-widow rolling average of the average total reward per session is calculated for "
-            f"further smoothing."
+            f"further smoothing.\n"
        )

-    with doc.create(Section("System Information")):
-        with doc.create(Subsection("Python")):
-            with doc.create(Tabular("|l|l|")) as table:
-                table.add_hline()
-                table.add_row((bold("Version"), sys.version))
-                table.add_hline()
+        file.write("## 2 System Information\n")
+        i = 1
+        file.write(f"### 2.{i} Python\n")
+        file.write(f"**Version:** {sys.version}\n")
+
        for section, section_data in data["system_info"].items():
+            i += 1
            if section_data:
-                with doc.create(Subsection(section)):
-                    if isinstance(section_data, dict):
-                        with doc.create(Tabular("|l|l|")) as table:
-                            table.add_hline()
-                            for key, value in section_data.items():
-                                table.add_row((bold(key), value))
-                                table.add_hline()
-                    elif isinstance(section_data, list):
-                        headers = section_data[0].keys()
-                        tabs_str = "|".join(["l" for _ in range(len(headers))])
-                        tabs_str = f"|{tabs_str}|"
-                        with doc.create(Tabular(tabs_str)) as table:
-                            table.add_hline()
-                            table.add_row([bold(h) for h in headers])
-                            table.add_hline()
-                            for item in section_data:
-                                table.add_row(item.values())
-                                table.add_hline()
+                file.write(f"### 2.{i} {section}\n")
+                if isinstance(section_data, dict):
+                    for key, value in section_data.items():
+                        file.write(f"- **{key}:** {value}\n")

-    headers_map = {
-        "total_sessions": "Total Sessions",
-        "total_episodes": "Total Episodes",
-        "total_time_steps": "Total Steps",
-        "av_s_per_session": "Av Session Duration (s)",
-        "av_s_per_step": "Av Step Duration (s)",
-        "av_s_per_100_steps_10_nodes": "Av Duration per 100 Steps per 10 Nodes (s)",
-    }
-    with doc.create(Section("Stats")):
-        with doc.create(Subsection("Benchmark Results")):
-            with doc.create(Tabular("|l|l|")) as table:
-                table.add_hline()
-                for section, header in headers_map.items():
-                    if section.startswith("av_"):
-                        table.add_row((bold(header), f"{data[section]:.4f}"))
-                    else:
-                        table.add_row((bold(header), data[section]))
-                    table.add_hline()
+        headers_map = {
+            "total_sessions": "Total Sessions",
+            "total_episodes": "Total Episodes",
+            "total_time_steps": "Total Steps",
+            "av_s_per_session": "Av Session Duration (s)",
+            "av_s_per_step": "Av Step Duration (s)",
+            "av_s_per_100_steps_10_nodes": "Av Duration per 100 Steps per 10 Nodes (s)",
+        }

-    with doc.create(Section("Graphs")):
-        with doc.create(Subsection(f"v{primaite_version} Learning Benchmark Plot")):
-            with doc.create(LatexFigure(position="h!")) as pic:
-                pic.add_image(str(this_version_plot_path))
-                pic.add_caption(f"PrimAITE {primaite_version} Learning Benchmark Plot")
+        file.write("## 3 Stats\n")
+        for section, header in headers_map.items():
+            if section.startswith("av_"):
+                file.write(f"- **{header}:** {data[section]:.4f}\n")
+            else:
+                file.write(f"- **{header}:** {data[section]}\n")

-        with doc.create(Subsection(f"Learning Benchmarking of All Released Versions under Major v{major_v}.*.*")):
-            with doc.create(LatexFigure(position="h!")) as pic:
-                pic.add_image(str(all_version_plot_path))
-                pic.add_caption(f"Learning Benchmarking of All Released Versions under Major v{major_v}.*.*")
+        file.write("## 4 Graphs\n")

-    doc.generate_pdf(str(this_version_plot_path).replace(".png", ""), clean_tex=True)
+        file.write(f"### 4.1 v{primaite_version} Learning Benchmark Plot\n")
+        file.write(f"![PrimAITE {primaite_version} Learning Benchmark Plot]({this_version_plot_path.name})\n")
+
+        file.write(f"### 4.2 Learning Benchmarking of All Released Versions under Major v{major_v}.#.#\n")
+        file.write(
+            f"![Learning Benchmarking of All Released Versions under "
+            f"Major v{major_v}.#.#]({all_version_plot_path.name})\n"
+        )
--- a/docs/source/simulation_components/system/common/common_configuration.rst
+++ b/docs/source/simulation_components/system/common/common_configuration.rst
@@ -16,3 +16,12 @@ The type of software that should be added. To add |SOFTWARE_NAME| this must be |
 ===========

 The configuration options are the attributes that fall under the options for an application.
+
+
+
+``fix_duration``
+""""""""""""""""
+
+Optional. Default value is ``2``.
+
+The number of timesteps the |SOFTWARE_NAME| will remain in a ``FIXING`` state before going into a ``GOOD`` state.
--- a/docs/source/simulation_components/system/list_of_applications.rst
+++ b/docs/source/simulation_components/system/list_of_applications.rst
@@ -8,7 +8,7 @@

    applications/*

-More info :py:mod:`primaite.game.game.APPLICATION_TYPES_MAPPING`
+More info :py:mod:`primaite.simulator.system.applications.application.Application`

 .. include:: list_of_system_applications.rst

--- a/pyproject.toml
+++ b/pyproject.toml
@@ -64,7 +64,6 @@ dev = [
    "gputil==1.4.0",
    "pip-licenses==4.3.0",
    "pre-commit==2.20.0",
-    "pylatex==1.4.1",
    "pytest==7.2.0",
    "pytest-xdist==3.3.1",
    "pytest-cov==4.0.0",
@@ -73,7 +72,9 @@ dev = [
    "Sphinx==7.1.2",
    "sphinx-copybutton==0.5.2",
    "wheel==0.38.4",
-    "nbsphinx==0.9.4"
+    "nbsphinx==0.9.4",
+    "nbmake==1.5.4",
+    "pytest-xdist==3.3.1"
 ]

 [project.scripts]
--- a/src/primaite/config/_package_data/data_manipulation.yaml
+++ b/src/primaite/config/_package_data/data_manipulation.yaml
@@ -739,8 +739,6 @@ agents:
          options:
            agent_name: client_2_green_user

-
-
    agent_settings:
      flatten_obs: true

--- a/src/primaite/game/agent/actions.py
+++ b/src/primaite/game/agent/actions.py
@@ -14,9 +14,10 @@ from abc import ABC, abstractmethod
 from typing import Dict, List, Literal, Optional, Tuple, TYPE_CHECKING, Union

 from gymnasium import spaces
-from pydantic import BaseModel, Field, field_validator, ValidationInfo
+from pydantic import BaseModel, ConfigDict, Field, field_validator, ValidationInfo

 from primaite import getLogger
+from primaite.interface.request import RequestFormat

 _LOGGER = getLogger(__name__)

@@ -228,7 +229,7 @@ class NodeApplicationInstallAction(AbstractAction):
        super().__init__(manager=manager)
        self.shape: Dict[str, int] = {"node_id": num_nodes}

-    def form_request(self, node_id: int, application_name: str, ip_address: str) -> List[str]:
+    def form_request(self, node_id: int, application_name: str) -> List[str]:
        """Return the action formatted as a request which can be ingested by the PrimAITE simulation."""
        node_name = self.manager.get_node_name_by_idx(node_id)
        if node_name is None:
@@ -241,10 +242,81 @@ class NodeApplicationInstallAction(AbstractAction):
            "application",
            "install",
            application_name,
-            ip_address,
        ]


+class ConfigureDatabaseClientAction(AbstractAction):
+    """Action which sets config parameters for a database client on a node."""
+
+    class _Opts(BaseModel):
+        """Schema for options that can be passed to this action."""
+
+        model_config = ConfigDict(extra="forbid")
+        server_ip_address: Optional[str] = None
+        server_password: Optional[str] = None
+
+    def __init__(self, manager: "ActionManager", **kwargs) -> None:
+        super().__init__(manager=manager)
+
+    def form_request(self, node_id: int, config: Dict) -> RequestFormat:
+        """Return the action formatted as a request that can be ingested by the simulation."""
+        node_name = self.manager.get_node_name_by_idx(node_id)
+        if node_name is None:
+            return ["do_nothing"]
+        ConfigureDatabaseClientAction._Opts.model_validate(config)  # check that options adhere to schema
+        return ["network", "node", node_name, "application", "DatabaseClient", "configure", config]
+
+
+class ConfigureRansomwareScriptAction(AbstractAction):
+    """Action which sets config parameters for a ransomware script on a node."""
+
+    class _Opts(BaseModel):
+        """Schema for options that can be passed to this option."""
+
+        model_config = ConfigDict(extra="forbid")
+        server_ip_address: Optional[str] = None
+        server_password: Optional[str] = None
+        payload: Optional[str] = None
+
+    def __init__(self, manager: "ActionManager", **kwargs) -> None:
+        super().__init__(manager=manager)
+
+    def form_request(self, node_id: int, config: Dict) -> RequestFormat:
+        """Return the action formatted as a request that can be ingested by the simulation."""
+        node_name = self.manager.get_node_name_by_idx(node_id)
+        if node_name is None:
+            return ["do_nothing"]
+        ConfigureRansomwareScriptAction._Opts.model_validate(config)  # check that options adhere to schema
+        return ["network", "node", node_name, "application", "RansomwareScript", "configure", config]
+
+
+class ConfigureDoSBotAction(AbstractAction):
+    """Action which sets config parameters for a DoS bot on a node."""
+
+    class _Opts(BaseModel):
+        """Schema for options that can be passed to this option."""
+
+        model_config = ConfigDict(extra="forbid")
+        target_ip_address: Optional[str] = None
+        target_port: Optional[str] = None
+        payload: Optional[str] = None
+        repeat: Optional[bool] = None
+        port_scan_p_of_success: Optional[float] = None
+        dos_intensity: Optional[float] = None
+        max_sessions: Optional[int] = None
+
+    def __init__(self, manager: "ActionManager", **kwargs) -> None:
+        super().__init__(manager=manager)
+
+    def form_request(self, node_id: int, config: Dict) -> RequestFormat:
+        """Return the action formatted as a request that can be ingested by the simulation."""
+        node_name = self.manager.get_node_name_by_idx(node_id)
+        if node_name is None:
+            return ["do_nothing"]
+        self._Opts.model_validate(config)  # check that options adhere to schema
+        return ["network", "node", node_name, "application", "DoSBot", "configure", config]
+
+
 class NodeApplicationRemoveAction(AbstractAction):
    """Action which removes/uninstalls an application."""

@@ -1045,6 +1117,9 @@ class ActionManager:
        "NODE_NMAP_PING_SCAN": NodeNMAPPingScanAction,
        "NODE_NMAP_PORT_SCAN": NodeNMAPPortScanAction,
        "NODE_NMAP_NETWORK_SERVICE_RECON": NodeNetworkServiceReconAction,
+        "CONFIGURE_DATABASE_CLIENT": ConfigureDatabaseClientAction,
+        "CONFIGURE_RANSOMWARE_SCRIPT": ConfigureRansomwareScriptAction,
+        "CONFIGURE_DOSBOT": ConfigureDoSBotAction,
    }
    """Dictionary which maps action type strings to the corresponding action class."""

--- a/src/primaite/game/agent/rewards.py
+++ b/src/primaite/game/agent/rewards.py
@@ -360,6 +360,38 @@ class SharedReward(AbstractReward):
        return cls(agent_name=agent_name)


+class ActionPenalty(AbstractReward):
+    """Apply a negative reward when taking any action except DONOTHING."""
+
+    def __init__(self, action_penalty: float, do_nothing_penalty: float) -> None:
+        """
+        Initialise the reward.
+
+        Reward or penalise agents for doing nothing or taking actions.
+
+        :param action_penalty: Reward to give agents for taking any action except DONOTHING
+        :type action_penalty: float
+        :param do_nothing_penalty: Reward to give agent for taking the DONOTHING action
+        :type do_nothing_penalty: float
+        """
+        self.action_penalty = action_penalty
+        self.do_nothing_penalty = do_nothing_penalty
+
+    def calculate(self, state: Dict, last_action_response: "AgentHistoryItem") -> float:
+        """Calculate the penalty to be applied."""
+        if last_action_response.action == "DONOTHING":
+            return self.do_nothing_penalty
+        else:
+            return self.action_penalty
+
+    @classmethod
+    def from_config(cls, config: Dict) -> "ActionPenalty":
+        """Build the ActionPenalty object from config."""
+        action_penalty = config.get("action_penalty", -1.0)
+        do_nothing_penalty = config.get("do_nothing_penalty", 0.0)
+        return cls(action_penalty=action_penalty, do_nothing_penalty=do_nothing_penalty)
+
+
 class RewardFunction:
    """Manages the reward function for the agent."""

@@ -370,6 +402,7 @@ class RewardFunction:
        "WEBPAGE_UNAVAILABLE_PENALTY": WebpageUnavailablePenalty,
        "GREEN_ADMIN_DATABASE_UNREACHABLE_PENALTY": GreenAdminDatabaseUnreachablePenalty,
        "SHARED_REWARD": SharedReward,
+        "ACTION_PENALTY": ActionPenalty,
    }
    """List of reward class identifiers."""

--- a/src/primaite/game/agent/scripted_agents/tap001.py
+++ b/src/primaite/game/agent/scripted_agents/tap001.py
@@ -55,7 +55,6 @@ class TAP001(AbstractScriptedAgent):
            return "NODE_APPLICATION_INSTALL", {
                "node_id": self.starting_node_idx,
                "application_name": "RansomwareScript",
-                "ip_address": self.ip_address,
            }

        return "NODE_APPLICATION_EXECUTE", {"node_id": self.starting_node_idx, "application_id": 0}
--- a/src/primaite/game/game.py
+++ b/src/primaite/game/game.py
@@ -26,11 +26,14 @@ from primaite.simulator.network.hardware.nodes.network.wireless_router import Wi
 from primaite.simulator.network.nmne import NmneData, store_nmne_config
 from primaite.simulator.network.transmission.transport_layer import Port
 from primaite.simulator.sim_container import Simulation
-from primaite.simulator.system.applications.database_client import DatabaseClient
-from primaite.simulator.system.applications.red_applications.data_manipulation_bot import DataManipulationBot
-from primaite.simulator.system.applications.red_applications.dos_bot import DoSBot
-from primaite.simulator.system.applications.red_applications.ransomware_script import RansomwareScript
-from primaite.simulator.system.applications.web_browser import WebBrowser
+from primaite.simulator.system.applications.application import Application
+from primaite.simulator.system.applications.database_client import DatabaseClient  # noqa: F401
+from primaite.simulator.system.applications.red_applications.data_manipulation_bot import (  # noqa: F401
+    DataManipulationBot,
+)
+from primaite.simulator.system.applications.red_applications.dos_bot import DoSBot  # noqa: F401
+from primaite.simulator.system.applications.red_applications.ransomware_script import RansomwareScript  # noqa: F401
+from primaite.simulator.system.applications.web_browser import WebBrowser  # noqa: F401
 from primaite.simulator.system.services.database.database_service import DatabaseService
 from primaite.simulator.system.services.dns.dns_client import DNSClient
 from primaite.simulator.system.services.dns.dns_server import DNSServer
@@ -42,15 +45,6 @@ from primaite.simulator.system.services.web_server.web_server import WebServer

 _LOGGER = getLogger(__name__)

-APPLICATION_TYPES_MAPPING = {
-    "WebBrowser": WebBrowser,
-    "DatabaseClient": DatabaseClient,
-    "DataManipulationBot": DataManipulationBot,
-    "DoSBot": DoSBot,
-    "RansomwareScript": RansomwareScript,
-}
-"""List of available applications that can be installed on nodes in the PrimAITE Simulation."""
-
 SERVICE_TYPES_MAPPING = {
    "DNSClient": DNSClient,
    "DNSServer": DNSServer,
@@ -302,6 +296,10 @@ class PrimaiteGame:
                        new_node.software_manager.install(SERVICE_TYPES_MAPPING[service_type])
                        new_service = new_node.software_manager.software[service_type]

+                        # fixing duration for the service
+                        if "fix_duration" in service_cfg.get("options", {}):
+                            new_service.fixing_duration = service_cfg["options"]["fix_duration"]
+
                        # start the service
                        new_service.start()
                    else:
@@ -324,7 +322,8 @@ class PrimaiteGame:
                        if "options" in service_cfg:
                            opt = service_cfg["options"]
                            new_service.password = opt.get("db_password", None)
-                            new_service.configure_backup(backup_server=IPv4Address(opt.get("backup_server_ip")))
+                            if "backup_server_ip" in opt:
+                                new_service.configure_backup(backup_server=IPv4Address(opt.get("backup_server_ip")))
                    if service_type == "FTPServer":
                        if "options" in service_cfg:
                            opt = service_cfg["options"]
@@ -338,9 +337,13 @@ class PrimaiteGame:
                    new_application = None
                    application_type = application_cfg["type"]

-                    if application_type in APPLICATION_TYPES_MAPPING:
-                        new_node.software_manager.install(APPLICATION_TYPES_MAPPING[application_type])
-                        new_application = new_node.software_manager.software[application_type]
+                    if application_type in Application._application_registry:
+                        new_node.software_manager.install(Application._application_registry[application_type])
+                        new_application = new_node.software_manager.software[application_type]  # grab the instance
+
+                        # fixing duration for the application
+                        if "fix_duration" in application_cfg.get("options", {}):
+                            new_application.fixing_duration = application_cfg["options"]["fix_duration"]
                    else:
                        msg = f"Configuration contains an invalid application type: {application_type}"
                        _LOGGER.error(msg)
@@ -363,7 +366,7 @@ class PrimaiteGame:
                        if "options" in application_cfg:
                            opt = application_cfg["options"]
                            new_application.configure(
-                                server_ip_address=IPv4Address(opt.get("server_ip")),
+                                server_ip_address=IPv4Address(opt.get("server_ip")) if opt.get("server_ip") else None,
                                server_password=opt.get("server_password"),
                                payload=opt.get("payload", "ENCRYPT"),
                            )
--- a/src/primaite/notebooks/Data-Manipulation-E2E-Demonstration.ipynb
+++ b/src/primaite/notebooks/Data-Manipulation-E2E-Demonstration.ipynb
@@ -507,8 +507,8 @@
   "cell_type": "markdown",
   "metadata": {},
   "source": [
-    "Now service 1 on node 2 has `health_status = 3`, indicating that the webapp is compromised.\n",
-    "File 1 in folder 1 on node 3 has `health_status = 2`, indicating that the database file is compromised."
+    "Now service 1 on HOST1 has `health_status = 3`, indicating that the webapp is compromised.\n",
+    "File 1 in folder 1 on HOST2 has `health_status = 2`, indicating that the database file is compromised."
   ]
  },
  {
@@ -545,9 +545,9 @@
   "source": [
    "The fixing takes two steps, so the reward hasn't changed yet. Let's do nothing for another timestep, the reward should improve.\n",
    "\n",
-    "The reward will increase slightly as soon as the file finishes restoring. Then, the reward will increase to 1 when both green agents make successful requests.\n",
+    "The reward will increase slightly as soon as the file finishes restoring. Then, the reward will increase to 0.9 when both green agents make successful requests.\n",
    "\n",
-    "Run the following cell until the green action is `NODE_APPLICATION_EXECUTE` for application 0, then the reward should become 1. If you run it enough times, another red attack will happen and the reward will drop again."
+    "Run the following cell until the green action is `NODE_APPLICATION_EXECUTE` for application 0, then the reward should increase. If you run it enough times, another red attack will happen and the reward will drop again."
   ]
  },
  {
@@ -708,7 +708,7 @@
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.10.12"
  }
 },
 "nbformat": 4,
--- a/src/primaite/notebooks/multi-processing.ipynb
+++ b/src/primaite/notebooks/multi-processing.ipynb
@@ -143,7 +143,7 @@
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.10.11"
  }
 },
 "nbformat": 4,
--- a/src/primaite/simulator/_package_data/create-simulation_demo.ipynb
+++ b/src/primaite/simulator/_package_data/create-simulation_demo.ipynb
@@ -171,7 +171,7 @@
    "from primaite.simulator.file_system.file_system import FileSystem\n",
    "\n",
    "# no applications exist yet so we will create our own.\n",
-    "class MSPaint(Application):\n",
+    "class MSPaint(Application, identifier=\"MSPaint\"):\n",
    "    def describe_state(self):\n",
    "        return super().describe_state()"
   ]
--- a/src/primaite/simulator/core.py
+++ b/src/primaite/simulator/core.py
@@ -196,7 +196,7 @@ class SimComponent(BaseModel):

        ..code::python

-            class WebBrowser(Application):
+            class WebBrowser(Application, identifier="WebBrowser"):
            def _init_request_manager(self) -> RequestManager:
                rm = super()._init_request_manager() # all requests generic to any Application get initialised
                rm.add_request(...) # initialise any requests specific to the web browser
--- a/src/primaite/simulator/network/hardware/base.py
+++ b/src/primaite/simulator/network/hardware/base.py
@@ -6,7 +6,7 @@ import secrets
 from abc import ABC, abstractmethod
 from ipaddress import IPv4Address, IPv4Network
 from pathlib import Path
-from typing import Any, ClassVar, Dict, Optional, Type, TypeVar, Union
+from typing import Any, ClassVar, Dict, Optional, TypeVar, Union

 from prettytable import MARKDOWN, PrettyTable
 from pydantic import BaseModel, Field
@@ -878,6 +878,61 @@ class Node(SimComponent):

        More information in user guide and docstring for SimComponent._init_request_manager.
        """
+
+        def _install_application(request: RequestFormat, context: Dict) -> RequestResponse:
+            """
+            Allows agents to install applications to the node.
+
+            :param request: list containing the application name as the only element
+            :type request: RequestFormat
+            :param context: additional context for resolving this action, currently unused
+            :type context: dict
+            :return: Request response with a success code if the application was installed.
+            :rtype: RequestResponse
+            """
+            application_name = request[0]
+            if self.software_manager.software.get(application_name):
+                self.sys_log.warning(f"Can't install {application_name}. It's already installed.")
+                return RequestResponse.from_bool(False)
+            application_class = Application._application_registry[application_name]
+            self.software_manager.install(application_class)
+            application_instance = self.software_manager.software.get(application_name)
+            self.applications[application_instance.uuid] = application_instance
+            _LOGGER.debug(f"Added application {application_instance.name} to node {self.hostname}")
+            self._application_request_manager.add_request(
+                application_name, RequestType(func=application_instance._request_manager)
+            )
+            application_instance.install()
+            if application_name in self.software_manager.software:
+                return RequestResponse.from_bool(True)
+            else:
+                return RequestResponse.from_bool(False)
+
+        def _uninstall_application(request: RequestFormat, context: Dict) -> RequestResponse:
+            """
+            Uninstall and completely remove application from this node.
+
+            This method is useful for allowing agents to take this action.
+
+            :param request: list containing the application name as the only element
+            :type request: RequestFormat
+            :param context: additional context for resolving this action, currently unused
+            :type context: dict
+            :return: Request response with a success code if the application was uninstalled.
+            :rtype: RequestResponse
+            """
+            application_name = request[0]
+            if application_name not in self.software_manager.software:
+                self.sys_log.warning(f"Can't uninstall {application_name}. It's not installed.")
+                return RequestResponse.from_bool(False)
+
+            application_instance = self.software_manager.software.get(application_name)
+            self.software_manager.uninstall(application_instance.name)
+            if application_instance.name not in self.software_manager.software:
+                return RequestResponse.from_bool(True)
+            else:
+                return RequestResponse.from_bool(False)
+
        _node_is_on = Node._NodeIsOnValidator(node=self)

        rm = super()._init_request_manager()
@@ -934,25 +989,8 @@ class Node(SimComponent):
            name="application", request_type=RequestType(func=self._application_manager)
        )

-        self._application_manager.add_request(
-            name="install",
-            request_type=RequestType(
-                func=lambda request, context: RequestResponse.from_bool(
-                    self.application_install_action(
-                        application=self._read_application_type(request[0]), ip_address=request[1]
-                    )
-                )
-            ),
-        )
-
-        self._application_manager.add_request(
-            name="uninstall",
-            request_type=RequestType(
-                func=lambda request, context: RequestResponse.from_bool(
-                    self.application_uninstall_action(application=self._read_application_type(request[0]))
-                )
-            ),
-        )
+        self._application_manager.add_request(name="install", request_type=RequestType(func=_install_application))
+        self._application_manager.add_request(name="uninstall", request_type=RequestType(func=_uninstall_application))

        return rm

@@ -960,29 +998,6 @@ class Node(SimComponent):
        """Install System Software - software that is usually provided with the OS."""
        pass

-    def _read_application_type(self, application_class_str: str) -> Type[IOSoftwareClass]:
-        """Wrapper that converts the string from the request manager into the appropriate class for the application."""
-        if application_class_str == "DoSBot":
-            from primaite.simulator.system.applications.red_applications.dos_bot import DoSBot
-
-            return DoSBot
-        elif application_class_str == "DataManipulationBot":
-            from primaite.simulator.system.applications.red_applications.data_manipulation_bot import (
-                DataManipulationBot,
-            )
-
-            return DataManipulationBot
-        elif application_class_str == "WebBrowser":
-            from primaite.simulator.system.applications.web_browser import WebBrowser
-
-            return WebBrowser
-        elif application_class_str == "RansomwareScript":
-            from primaite.simulator.system.applications.red_applications.ransomware_script import RansomwareScript
-
-            return RansomwareScript
-        else:
-            return 0
-
    def describe_state(self) -> Dict:
        """
        Produce a dictionary describing the current state of this object.
@@ -1411,76 +1426,6 @@ class Node(SimComponent):
        self.sys_log.info(f"Uninstalled application {application.name}")
        self._application_request_manager.remove_request(application.name)

-    def application_install_action(self, application: Application, ip_address: Optional[str] = None) -> bool:
-        """
-        Install an application on this node and configure it.
-
-        This method is useful for allowing agents to take this action.
-
-        :param application: Application object that has not been installed on any node yet.
-        :type application: Application
-        :param ip_address: IP address used to configure the application
-        (target IP for the DoSBot or server IP for the DataManipulationBot)
-        :type ip_address: str
-        :return: True if the application is installed successfully, otherwise False.
-        """
-        if application in self:
-            _LOGGER.warning(
-                f"Can't add application {application.__name__}" + f"to node {self.hostname}. It's already installed."
-            )
-            return True
-
-        self.software_manager.install(application)
-        application_instance = self.software_manager.software.get(str(application.__name__))
-        self.applications[application_instance.uuid] = application_instance
-        _LOGGER.debug(f"Added application {application_instance.name} to node {self.hostname}")
-        self._application_request_manager.add_request(
-            application_instance.name, RequestType(func=application_instance._request_manager)
-        )
-
-        # Configure application if additional parameters are given
-        if ip_address:
-            if application_instance.name == "DoSBot":
-                application_instance.configure(target_ip_address=IPv4Address(ip_address))
-            elif application_instance.name == "DataManipulationBot":
-                application_instance.configure(server_ip_address=IPv4Address(ip_address))
-            elif application_instance.name == "RansomwareScript":
-                application_instance.configure(server_ip_address=IPv4Address(ip_address))
-            else:
-                pass
-        application_instance.install()
-        if application_instance.name in self.software_manager.software:
-            return True
-        else:
-            return False
-
-    def application_uninstall_action(self, application: Application) -> bool:
-        """
-        Uninstall and completely remove application from this node.
-
-        This method is useful for allowing agents to take this action.
-
-        :param application: Application object that is currently associated with this node.
-        :type application: Application
-        :return: True if the application is uninstalled successfully, otherwise False.
-        """
-        if application.__name__ not in self.software_manager.software:
-            _LOGGER.warning(
-                f"Can't remove application {application.__name__}" + f"from node {self.hostname}. It's not installed."
-            )
-            return True
-
-        application_instance = self.software_manager.software.get(
-            str(application.__name__)
-        )  # This works because we can't have two applications with the same name on the same node
-        # self.uninstall_application(application_instance)
-        self.software_manager.uninstall(application_instance.name)
-
-        if application_instance.name not in self.software_manager.software:
-            return True
-        else:
-            return False
-
    def _shut_down_actions(self):
        """Actions to perform when the node is shut down."""
        # Turn off all the services in the node
--- a/src/primaite/simulator/system/applications/application.py
+++ b/src/primaite/simulator/system/applications/application.py
@@ -1,7 +1,7 @@
 # © Crown-owned copyright 2024, Defence Science and Technology Laboratory UK
 from abc import abstractmethod
 from enum import Enum
-from typing import Any, Dict, Optional, Set
+from typing import Any, ClassVar, Dict, Optional, Set, Type

 from primaite.interface.request import RequestResponse
 from primaite.simulator.core import RequestManager, RequestType
@@ -39,6 +39,22 @@ class Application(IOSoftware):
    install_countdown: Optional[int] = None
    "The countdown to the end of the installation process. None if not currently installing"

+    _application_registry: ClassVar[Dict[str, Type["Application"]]] = {}
+    """Registry of application types. Automatically populated when subclasses are defined."""
+
+    def __init_subclass__(cls, identifier: str, **kwargs: Any) -> None:
+        """
+        Register an application type.
+
+        :param identifier: Uniquely specifies an application class by name. Used for finding items by config.
+        :type identifier: str
+        :raises ValueError: When attempting to register an application with a name that is already allocated.
+        """
+        super().__init_subclass__(**kwargs)
+        if identifier in cls._application_registry:
+            raise ValueError(f"Tried to define new application {identifier}, but this name is already reserved.")
+        cls._application_registry[identifier] = cls
+
    def __init__(self, **kwargs):
        super().__init__(**kwargs)

--- a/src/primaite/simulator/system/applications/database_client.py
+++ b/src/primaite/simulator/system/applications/database_client.py
@@ -8,13 +8,14 @@ from uuid import uuid4
 from prettytable import MARKDOWN, PrettyTable
 from pydantic import BaseModel

-from primaite.interface.request import RequestResponse
+from primaite.interface.request import RequestFormat, RequestResponse
 from primaite.simulator.core import RequestManager, RequestType
 from primaite.simulator.network.hardware.nodes.host.host_node import HostNode
 from primaite.simulator.network.transmission.network_layer import IPProtocol
 from primaite.simulator.network.transmission.transport_layer import Port
 from primaite.simulator.system.applications.application import Application
 from primaite.simulator.system.core.software_manager import SoftwareManager
+from primaite.utils.validators import IPV4Address


 class DatabaseClientConnection(BaseModel):
@@ -54,7 +55,7 @@ class DatabaseClientConnection(BaseModel):
            self.client._disconnect(self.connection_id)  # noqa


-class DatabaseClient(Application):
+class DatabaseClient(Application, identifier="DatabaseClient"):
    """
    A DatabaseClient application.

@@ -96,6 +97,14 @@ class DatabaseClient(Application):
        """
        rm = super()._init_request_manager()
        rm.add_request("execute", RequestType(func=lambda request, context: RequestResponse.from_bool(self.execute())))
+
+        def _configure(request: RequestFormat, context: Dict) -> RequestResponse:
+            ip, pw = request[-1].get("server_ip_address"), request[-1].get("server_password")
+            ip = None if ip is None else IPV4Address(ip)
+            success = self.configure(server_ip_address=ip, server_password=pw)
+            return RequestResponse.from_bool(success)
+
+        rm.add_request("configure", RequestType(func=_configure))
        return rm

    def execute(self) -> bool:
@@ -141,16 +150,17 @@ class DatabaseClient(Application):
            table.add_row([connection_id, connection.is_active])
        print(table.get_string(sortby="Connection ID"))

-    def configure(self, server_ip_address: IPv4Address, server_password: Optional[str] = None):
+    def configure(self, server_ip_address: Optional[IPv4Address] = None, server_password: Optional[str] = None) -> bool:
        """
        Configure the DatabaseClient to communicate with a DatabaseService.

        :param server_ip_address: The IP address of the Node the DatabaseService is on.
        :param server_password: The password on the DatabaseService.
        """
-        self.server_ip_address = server_ip_address
-        self.server_password = server_password
+        self.server_ip_address = server_ip_address or self.server_ip_address
+        self.server_password = server_password or self.server_password
        self.sys_log.info(f"{self.name}: Configured the {self.name} with {server_ip_address=}, {server_password=}.")
+        return True

    def connect(self) -> bool:
        """Connect the native client connection."""
--- a/src/primaite/simulator/system/applications/nmap.py
+++ b/src/primaite/simulator/system/applications/nmap.py
@@ -44,7 +44,7 @@ class PortScanPayload(SimComponent):
        return state


-class NMAP(Application):
+class NMAP(Application, identifier="NMAP"):
    """
    A class representing the NMAP application for network scanning.

--- a/src/primaite/simulator/system/applications/red_applications/data_manipulation_bot.py
+++ b/src/primaite/simulator/system/applications/red_applications/data_manipulation_bot.py
@@ -37,7 +37,7 @@ class DataManipulationAttackStage(IntEnum):
    "Signifies that the attack has failed."


-class DataManipulationBot(Application):
+class DataManipulationBot(Application, identifier="DataManipulationBot"):
    """A bot that simulates a script which performs a SQL injection attack."""

    payload: Optional[str] = None
--- a/src/primaite/simulator/system/applications/red_applications/dos_bot.py
+++ b/src/primaite/simulator/system/applications/red_applications/dos_bot.py
@@ -1,11 +1,11 @@
 # © Crown-owned copyright 2024, Defence Science and Technology Laboratory UK
 from enum import IntEnum
 from ipaddress import IPv4Address
-from typing import Optional
+from typing import Dict, Optional

 from primaite import getLogger
 from primaite.game.science import simulate_trial
-from primaite.interface.request import RequestResponse
+from primaite.interface.request import RequestFormat, RequestResponse
 from primaite.simulator.core import RequestManager, RequestType
 from primaite.simulator.network.transmission.transport_layer import Port
 from primaite.simulator.system.applications.database_client import DatabaseClient
@@ -29,7 +29,7 @@ class DoSAttackStage(IntEnum):
    "Attack is completed."


-class DoSBot(DatabaseClient):
+class DoSBot(DatabaseClient, identifier="DoSBot"):
    """A bot that simulates a Denial of Service attack."""

    target_ip_address: Optional[IPv4Address] = None
@@ -71,6 +71,24 @@ class DoSBot(DatabaseClient):
            request_type=RequestType(func=lambda request, context: RequestResponse.from_bool(self.run())),
        )

+        def _configure(request: RequestFormat, context: Dict) -> RequestResponse:
+            """
+            Configure the DoSBot.
+
+            :param request: List with one element that is a dict of options to pass to the configure method.
+            :type request: RequestFormat
+            :param context: additional context for resolving this action, currently unused
+            :type context: dict
+            :return: Request Response object with a success code determining if the configuration was successful.
+            :rtype: RequestResponse
+            """
+            if "target_ip_address" in request[-1]:
+                request[-1]["target_ip_address"] = IPv4Address(request[-1]["target_ip_address"])
+            if "target_port" in request[-1]:
+                request[-1]["target_port"] = Port[request[-1]["target_port"]]
+            return RequestResponse.from_bool(self.configure(**request[-1]))
+
+        rm.add_request("configure", request_type=RequestType(func=_configure))
        return rm

    def configure(
@@ -82,7 +100,7 @@ class DoSBot(DatabaseClient):
        port_scan_p_of_success: float = 0.1,
        dos_intensity: float = 1.0,
        max_sessions: int = 1000,
-    ):
+    ) -> bool:
        """
        Configure the Denial of Service bot.

@@ -90,10 +108,12 @@ class DoSBot(DatabaseClient):
        :param: target_port: The port of the target service. Optional - Default is `Port.HTTP`
        :param: payload: The payload the DoS Bot will throw at the target service. Optional - Default is `None`
        :param: repeat: If True, the bot will maintain the attack. Optional - Default is `True`
-        :param: port_scan_p_of_success: The chance of the port scan being sucessful. Optional - Default is 0.1 (10%)
+        :param: port_scan_p_of_success: The chance of the port scan being successful. Optional - Default is 0.1 (10%)
        :param: dos_intensity: The intensity of the DoS attack.
            Multiplied with the application's max session - Default is 1.0
        :param: max_sessions: The maximum number of sessions the DoS bot will attack with. Optional - Default is 1000
+        :return: Always returns True
+        :rtype: bool
        """
        self.target_ip_address = target_ip_address
        self.target_port = target_port
@@ -106,6 +126,7 @@ class DoSBot(DatabaseClient):
            f"{self.name}: Configured the {self.name} with {target_ip_address=}, {target_port=}, {payload=}, "
            f"{repeat=}, {port_scan_p_of_success=}, {dos_intensity=}, {max_sessions=}."
        )
+        return True

    def run(self) -> bool:
        """Run the Denial of Service Bot."""
@@ -117,6 +138,9 @@ class DoSBot(DatabaseClient):
        The main application loop for the Denial of Service bot.

        The loop goes through the stages of a DoS attack.
+
+        :return: True if the application loop could be executed, False otherwise.
+        :rtype: bool
        """
        if not self._can_perform_action():
            return False
@@ -126,7 +150,7 @@ class DoSBot(DatabaseClient):
            self.sys_log.warning(
                f"{self.name} is not properly configured. {self.target_ip_address=}, {self.target_port=}"
            )
-            return True
+            return False

        self.clear_connections()
        self._perform_port_scan(p_of_success=self.port_scan_p_of_success)
--- a/src/primaite/simulator/system/applications/red_applications/ransomware_script.py
+++ b/src/primaite/simulator/system/applications/red_applications/ransomware_script.py
@@ -2,7 +2,7 @@
 from ipaddress import IPv4Address
 from typing import Dict, Optional

-from primaite.interface.request import RequestResponse
+from primaite.interface.request import RequestFormat, RequestResponse
 from primaite.simulator.core import RequestManager, RequestType
 from primaite.simulator.network.transmission.network_layer import IPProtocol
 from primaite.simulator.network.transmission.transport_layer import Port
@@ -10,7 +10,7 @@ from primaite.simulator.system.applications.application import Application
 from primaite.simulator.system.applications.database_client import DatabaseClient, DatabaseClientConnection


-class RansomwareScript(Application):
+class RansomwareScript(Application, identifier="RansomwareScript"):
    """Ransomware Kill Chain - Designed to be used by the TAP001 Agent on the example layout Network.

    :ivar payload: The attack stage query payload. (Default ENCRYPT)
@@ -62,6 +62,25 @@ class RansomwareScript(Application):
            name="execute",
            request_type=RequestType(func=lambda request, context: RequestResponse.from_bool(self.attack())),
        )
+
+        def _configure(request: RequestFormat, context: Dict) -> RequestResponse:
+            """
+            Request for configuring the target database and payload.
+
+            :param request: Request with one element contianing a dict of parameters for the configure method.
+            :type request: RequestFormat
+            :param context: additional context for resolving this action, currently unused
+            :type context: dict
+            :return: RequestResponse object with a success code reflecting whether the configuration could be applied.
+            :rtype: RequestResponse
+            """
+            ip = request[-1].get("server_ip_address")
+            ip = None if ip is None else IPv4Address(ip)
+            pw = request[-1].get("server_password")
+            payload = request[-1].get("payload")
+            return RequestResponse.from_bool(self.configure(ip, pw, payload))
+
+        rm.add_request("configure", request_type=RequestType(func=_configure))
        return rm

    def run(self) -> bool:
@@ -88,10 +107,10 @@ class RansomwareScript(Application):

    def configure(
        self,
-        server_ip_address: IPv4Address,
+        server_ip_address: Optional[IPv4Address] = None,
        server_password: Optional[str] = None,
        payload: Optional[str] = None,
-    ):
+    ) -> bool:
        """
        Configure the Ransomware Script to communicate with a DatabaseService.

@@ -108,6 +127,7 @@ class RansomwareScript(Application):
        self.sys_log.info(
            f"{self.name}: Configured the {self.name} with {server_ip_address=}, {payload=}, {server_password=}."
        )
+        return True

    def attack(self) -> bool:
        """Perform the attack steps after opening the application."""
--- a/src/primaite/simulator/system/applications/web_browser.py
+++ b/src/primaite/simulator/system/applications/web_browser.py
@@ -23,7 +23,7 @@ from primaite.simulator.system.services.dns.dns_client import DNSClient
 _LOGGER = getLogger(__name__)


-class WebBrowser(Application):
+class WebBrowser(Application, identifier="WebBrowser"):
    """
    Represents a web browser in the simulation environment.

--- a/src/primaite/simulator/system/services/database/database_service.py
+++ b/src/primaite/simulator/system/services/database/database_service.py
@@ -197,7 +197,11 @@ class DatabaseService(Service):
            status_code = 503  # service unavailable
            if self.health_state_actual == SoftwareHealthState.OVERWHELMED:
                self.sys_log.error(f"{self.name}: Connect request for {src_ip=} declined. Service is at capacity.")
-            if self.health_state_actual == SoftwareHealthState.GOOD:
+            if self.health_state_actual in [
+                SoftwareHealthState.GOOD,
+                SoftwareHealthState.FIXING,
+                SoftwareHealthState.COMPROMISED,
+            ]:
                if self.password == password:
                    status_code = 200  # ok
                    connection_id = self._generate_connection_id()
@@ -244,6 +248,10 @@ class DatabaseService(Service):
            self.sys_log.error(f"{self.name}: Failed to run {query} because the database file is missing.")
            return {"status_code": 404, "type": "sql", "data": False}

+        if self.health_state_actual is not SoftwareHealthState.GOOD:
+            self.sys_log.error(f"{self.name}: Failed to run {query} because the database service is unavailable.")
+            return {"status_code": 500, "type": "sql", "data": False}
+
        if query == "SELECT":
            if self.db_file.health_status == FileSystemItemHealthStatus.CORRUPT:
                return {
--- a/tests/assets/configs/action_penalty.yaml
+++ b/tests/assets/configs/action_penalty.yaml
@@ -0,0 +1,792 @@
+io_settings:
+  save_agent_actions: false
+  save_step_metadata: false
+  save_pcap_logs: false
+  save_sys_logs: false
+
+
+game:
+  max_episode_length: 256
+  ports:
+  - HTTP
+  - POSTGRES_SERVER
+  protocols:
+  - ICMP
+  - TCP
+  - UDP
+  thresholds:
+    nmne:
+      high: 10
+      medium: 5
+      low: 0
+
+agents:
+
+  - ref: defender
+    team: BLUE
+    type: ProxyAgent
+
+    observation_space:
+      type: CUSTOM
+      options:
+        components:
+          - type: NODES
+            label: NODES
+            options:
+              hosts:
+                - hostname: domain_controller
+                - hostname: web_server
+                  services:
+                    - service_name: WebServer
+                - hostname: database_server
+                  folders:
+                    - folder_name: database
+                      files:
+                      - file_name: database.db
+                - hostname: backup_server
+                - hostname: security_suite
+                - hostname: client_1
+                - hostname: client_2
+              num_services: 1
+              num_applications: 0
+              num_folders: 1
+              num_files: 1
+              num_nics: 2
+              include_num_access: false
+              include_nmne: true
+              routers:
+                - hostname: router_1
+              num_ports: 0
+              ip_list:
+                - 192.168.1.10
+                - 192.168.1.12
+                - 192.168.1.14
+                - 192.168.1.16
+                - 192.168.1.110
+                - 192.168.10.21
+                - 192.168.10.22
+                - 192.168.10.110
+              wildcard_list:
+                - 0.0.0.1
+              port_list:
+                - 80
+                - 5432
+              protocol_list:
+                - ICMP
+                - TCP
+                - UDP
+              num_rules: 10
+
+          - type: LINKS
+            label: LINKS
+            options:
+              link_references:
+                - router_1:eth-1<->switch_1:eth-8
+                - router_1:eth-2<->switch_2:eth-8
+                - switch_1:eth-1<->domain_controller:eth-1
+                - switch_1:eth-2<->web_server:eth-1
+                - switch_1:eth-3<->database_server:eth-1
+                - switch_1:eth-4<->backup_server:eth-1
+                - switch_1:eth-7<->security_suite:eth-1
+                - switch_2:eth-1<->client_1:eth-1
+                - switch_2:eth-2<->client_2:eth-1
+                - switch_2:eth-7<->security_suite:eth-2
+          - type: "NONE"
+            label: ICS
+            options: {}
+
+    action_space:
+      action_list:
+        - type: DONOTHING
+        - type: NODE_SERVICE_SCAN
+        - type: NODE_SERVICE_STOP
+        - type: NODE_SERVICE_START
+        - type: NODE_SERVICE_PAUSE
+        - type: NODE_SERVICE_RESUME
+        - type: NODE_SERVICE_RESTART
+        - type: NODE_SERVICE_DISABLE
+        - type: NODE_SERVICE_ENABLE
+        - type: NODE_SERVICE_FIX
+        - type: NODE_FILE_SCAN
+        - type: NODE_FILE_CHECKHASH
+        - type: NODE_FILE_DELETE
+        - type: NODE_FILE_REPAIR
+        - type: NODE_FILE_RESTORE
+        - type: NODE_FOLDER_SCAN
+        - type: NODE_FOLDER_CHECKHASH
+        - type: NODE_FOLDER_REPAIR
+        - type: NODE_FOLDER_RESTORE
+        - type: NODE_OS_SCAN
+        - type: NODE_SHUTDOWN
+        - type: NODE_STARTUP
+        - type: NODE_RESET
+        - type: ROUTER_ACL_ADDRULE
+        - type: ROUTER_ACL_REMOVERULE
+        - type: HOST_NIC_ENABLE
+        - type: HOST_NIC_DISABLE
+
+      action_map:
+          0:
+            action: DONOTHING
+            options: {}
+          # scan webapp service
+          1:
+            action: NODE_SERVICE_SCAN
+            options:
+              node_id: 1
+              service_id: 0
+          # stop webapp service
+          2:
+            action: NODE_SERVICE_STOP
+            options:
+              node_id: 1
+              service_id: 0
+          # start webapp service
+          3:
+            action: "NODE_SERVICE_START"
+            options:
+              node_id: 1
+              service_id: 0
+          4:
+            action: "NODE_SERVICE_PAUSE"
+            options:
+              node_id: 1
+              service_id: 0
+          5:
+            action: "NODE_SERVICE_RESUME"
+            options:
+              node_id: 1
+              service_id: 0
+          6:
+            action: "NODE_SERVICE_RESTART"
+            options:
+              node_id: 1
+              service_id: 0
+          7:
+            action: "NODE_SERVICE_DISABLE"
+            options:
+              node_id: 1
+              service_id: 0
+          8:
+            action: "NODE_SERVICE_ENABLE"
+            options:
+              node_id: 1
+              service_id: 0
+          9: # check database.db file
+            action: "NODE_FILE_SCAN"
+            options:
+              node_id: 2
+              folder_id: 0
+              file_id: 0
+          10:
+            action: "NODE_FILE_CHECKHASH"
+            options:
+              node_id: 2
+              folder_id: 0
+              file_id: 0
+          11:
+            action: "NODE_FILE_DELETE"
+            options:
+              node_id: 2
+              folder_id: 0
+              file_id: 0
+          12:
+            action: "NODE_FILE_REPAIR"
+            options:
+              node_id: 2
+              folder_id: 0
+              file_id: 0
+          13:
+            action: "NODE_SERVICE_FIX"
+            options:
+              node_id: 2
+              service_id: 0
+          14:
+            action: "NODE_FOLDER_SCAN"
+            options:
+              node_id: 2
+              folder_id: 0
+          15:
+            action: "NODE_FOLDER_CHECKHASH"
+            options:
+              node_id: 2
+              folder_id: 0
+          16:
+            action: "NODE_FOLDER_REPAIR"
+            options:
+              node_id: 2
+              folder_id: 0
+          17:
+            action: "NODE_FOLDER_RESTORE"
+            options:
+              node_id: 2
+              folder_id: 0
+          18:
+            action: "NODE_OS_SCAN"
+            options:
+              node_id: 0
+          19:
+            action: "NODE_SHUTDOWN"
+            options:
+              node_id: 0
+          20:
+            action: NODE_STARTUP
+            options:
+              node_id: 0
+          21:
+            action: NODE_RESET
+            options:
+              node_id: 0
+          22:
+            action: "NODE_OS_SCAN"
+            options:
+              node_id: 1
+          23:
+            action: "NODE_SHUTDOWN"
+            options:
+              node_id: 1
+          24:
+            action: NODE_STARTUP
+            options:
+              node_id: 1
+          25:
+            action: NODE_RESET
+            options:
+              node_id: 1
+          26: # old action num: 18
+            action: "NODE_OS_SCAN"
+            options:
+                node_id: 2
+          27:
+            action: "NODE_SHUTDOWN"
+            options:
+              node_id: 2
+          28:
+            action: NODE_STARTUP
+            options:
+              node_id: 2
+          29:
+            action: NODE_RESET
+            options:
+              node_id: 2
+          30:
+            action: "NODE_OS_SCAN"
+            options:
+              node_id: 3
+          31:
+            action: "NODE_SHUTDOWN"
+            options:
+              node_id: 3
+          32:
+            action: NODE_STARTUP
+            options:
+              node_id: 3
+          33:
+            action: NODE_RESET
+            options:
+              node_id: 3
+          34:
+            action: "NODE_OS_SCAN"
+            options:
+              node_id: 4
+          35:
+            action: "NODE_SHUTDOWN"
+            options:
+              node_id: 4
+          36:
+            action: NODE_STARTUP
+            options:
+              node_id: 4
+          37:
+            action: NODE_RESET
+            options:
+              node_id: 4
+          38:
+            action: "NODE_OS_SCAN"
+            options:
+              node_id: 5
+          39: # old action num: 19 # shutdown client 1
+            action: "NODE_SHUTDOWN"
+            options:
+              node_id: 5
+          40: # old action num: 20
+            action: NODE_STARTUP
+            options:
+              node_id: 5
+          41: # old action num: 21
+            action: NODE_RESET
+            options:
+              node_id: 5
+          42:
+            action: "NODE_OS_SCAN"
+            options:
+              node_id: 6
+          43:
+            action: "NODE_SHUTDOWN"
+            options:
+              node_id: 6
+          44:
+            action: NODE_STARTUP
+            options:
+              node_id: 6
+          45:
+            action: NODE_RESET
+            options:
+              node_id: 6
+
+          46: # old action num: 22 # "ACL: ADDRULE - Block outgoing traffic from client 1"
+            action: "ROUTER_ACL_ADDRULE"
+            options:
+                target_router_nodename: router_1
+                position: 1
+                permission: 2
+                source_ip_id: 7 # client 1
+                dest_ip_id: 1 # ALL
+                source_port_id: 1
+                dest_port_id: 1
+                protocol_id: 1
+                source_wildcard_id: 0
+                dest_wildcard_id: 0
+          47: # old action num: 23 # "ACL: ADDRULE - Block outgoing traffic from client 2"
+            action: "ROUTER_ACL_ADDRULE"
+            options:
+                target_router_nodename: router_1
+                position: 2
+                permission: 2
+                source_ip_id: 8 # client 2
+                dest_ip_id: 1 # ALL
+                source_port_id: 1
+                dest_port_id: 1
+                protocol_id: 1
+                source_wildcard_id: 0
+                dest_wildcard_id: 0
+          48: # old action num: 24 # block tcp traffic from client 1 to web app
+            action: "ROUTER_ACL_ADDRULE"
+            options:
+                target_router_nodename: router_1
+                position: 3
+                permission: 2
+                source_ip_id: 7 # client 1
+                dest_ip_id: 3 # web server
+                source_port_id: 1
+                dest_port_id: 1
+                protocol_id: 3
+                source_wildcard_id: 0
+                dest_wildcard_id: 0
+          49: # old action num: 25 # block tcp traffic from client 2 to web app
+            action: "ROUTER_ACL_ADDRULE"
+            options:
+                target_router_nodename: router_1
+                position: 4
+                permission: 2
+                source_ip_id: 8 # client 2
+                dest_ip_id: 3 # web server
+                source_port_id: 1
+                dest_port_id: 1
+                protocol_id: 3
+                source_wildcard_id: 0
+                dest_wildcard_id: 0
+          50: # old action num: 26
+            action: "ROUTER_ACL_ADDRULE"
+            options:
+                target_router_nodename: router_1
+                position: 5
+                permission: 2
+                source_ip_id: 7 # client 1
+                dest_ip_id: 4 # database
+                source_port_id: 1
+                dest_port_id: 1
+                protocol_id: 3
+                source_wildcard_id: 0
+                dest_wildcard_id: 0
+          51: # old action num: 27
+            action: "ROUTER_ACL_ADDRULE"
+            options:
+                target_router_nodename: router_1
+                position: 6
+                permission: 2
+                source_ip_id: 8 # client 2
+                dest_ip_id: 4 # database
+                source_port_id: 1
+                dest_port_id: 1
+                protocol_id: 3
+                source_wildcard_id: 0
+                dest_wildcard_id: 0
+          52: # old action num: 28
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 0
+          53: # old action num: 29
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 1
+          54: # old action num: 30
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 2
+          55: # old action num: 31
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 3
+          56: # old action num: 32
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 4
+          57: # old action num: 33
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 5
+          58: # old action num: 34
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 6
+          59: # old action num: 35
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 7
+          60: # old action num: 36
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 8
+          61: # old action num: 37
+            action: "ROUTER_ACL_REMOVERULE"
+            options:
+                target_router_nodename: router_1
+                position: 9
+          62: # old action num: 38
+            action: "HOST_NIC_DISABLE"
+            options:
+                node_id: 0
+                nic_id: 0
+          63: # old action num: 39
+            action: "HOST_NIC_ENABLE"
+            options:
+                node_id: 0
+                nic_id: 0
+          64: # old action num: 40
+            action: "HOST_NIC_DISABLE"
+            options:
+                node_id: 1
+                nic_id: 0
+          65: # old action num: 41
+            action: "HOST_NIC_ENABLE"
+            options:
+                node_id: 1
+                nic_id: 0
+          66: # old action num: 42
+            action: "HOST_NIC_DISABLE"
+            options:
+                node_id: 2
+                nic_id: 0
+          67: # old action num: 43
+            action: "HOST_NIC_ENABLE"
+            options:
+                node_id: 2
+                nic_id: 0
+          68: # old action num: 44
+            action: "HOST_NIC_DISABLE"
+            options:
+                node_id: 3
+                nic_id: 0
+          69: # old action num: 45
+            action: "HOST_NIC_ENABLE"
+            options:
+                node_id: 3
+                nic_id: 0
+          70: # old action num: 46
+            action: "HOST_NIC_DISABLE"
+            options:
+                node_id: 4
+                nic_id: 0
+          71: # old action num: 47
+            action: "HOST_NIC_ENABLE"
+            options:
+                node_id: 4
+                nic_id: 0
+          72: # old action num: 48
+            action: "HOST_NIC_DISABLE"
+            options:
+                node_id: 4
+                nic_id: 1
+          73: # old action num: 49
+            action: "HOST_NIC_ENABLE"
+            options:
+                node_id: 4
+                nic_id: 1
+          74: # old action num: 50
+            action: "HOST_NIC_DISABLE"
+            options:
+                node_id: 5
+                nic_id: 0
+          75: # old action num: 51
+            action: "HOST_NIC_ENABLE"
+            options:
+                node_id: 5
+                nic_id: 0
+          76: # old action num: 52
+            action: "HOST_NIC_DISABLE"
+            options:
+                node_id: 6
+                nic_id: 0
+          77: # old action num: 53
+            action: "HOST_NIC_ENABLE"
+            options:
+                node_id: 6
+                nic_id: 0
+
+
+
+      options:
+        nodes:
+        - node_name: domain_controller
+        - node_name: web_server
+          applications:
+          - application_name: DatabaseClient
+          services:
+          - service_name: WebServer
+        - node_name: database_server
+          folders:
+          - folder_name: database
+            files:
+            - file_name: database.db
+          services:
+          - service_name: DatabaseService
+        - node_name: backup_server
+        - node_name: security_suite
+        - node_name: client_1
+        - node_name: client_2
+
+        max_folders_per_node: 2
+        max_files_per_folder: 2
+        max_services_per_node: 2
+        max_nics_per_node: 8
+        max_acl_rules: 10
+        ip_list:
+          - 192.168.1.10
+          - 192.168.1.12
+          - 192.168.1.14
+          - 192.168.1.16
+          - 192.168.1.110
+          - 192.168.10.21
+          - 192.168.10.22
+          - 192.168.10.110
+
+
+    reward_function:
+      reward_components:
+        - type: ACTION_PENALTY
+          weight: 1.0
+          options:
+            action_penalty: -0.75
+            do_nothing_penalty: 0.125
+
+
+    agent_settings:
+      flatten_obs: true
+
+
+
+simulation:
+  network:
+    nmne_config:
+      capture_nmne: true
+      nmne_capture_keywords:
+        - DELETE
+    nodes:
+
+    - hostname: router_1
+      type: router
+      num_ports: 5
+      ports:
+        1:
+          ip_address: 192.168.1.1
+          subnet_mask: 255.255.255.0
+        2:
+          ip_address: 192.168.10.1
+          subnet_mask: 255.255.255.0
+      acl:
+        18:
+          action: PERMIT
+          src_port: POSTGRES_SERVER
+          dst_port: POSTGRES_SERVER
+        19:
+          action: PERMIT
+          src_port: DNS
+          dst_port: DNS
+        20:
+          action: PERMIT
+          src_port: FTP
+          dst_port: FTP
+        21:
+          action: PERMIT
+          src_port: HTTP
+          dst_port: HTTP
+        22:
+          action: PERMIT
+          src_port: ARP
+          dst_port: ARP
+        23:
+          action: PERMIT
+          protocol: ICMP
+
+    - hostname: switch_1
+      type: switch
+      num_ports: 8
+
+    - hostname: switch_2
+      type: switch
+      num_ports: 8
+
+    - hostname: domain_controller
+      type: server
+      ip_address: 192.168.1.10
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.1.1
+      services:
+      - type: DNSServer
+        options:
+          domain_mapping:
+            arcd.com: 192.168.1.12 # web server
+
+    - hostname: web_server
+      type: server
+      ip_address: 192.168.1.12
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.1.1
+      dns_server: 192.168.1.10
+      services:
+      - type: WebServer
+      applications:
+      - type: DatabaseClient
+        options:
+          db_server_ip: 192.168.1.14
+
+
+    - hostname: database_server
+      type: server
+      ip_address: 192.168.1.14
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.1.1
+      dns_server: 192.168.1.10
+      services:
+      - type: DatabaseService
+        options:
+          backup_server_ip: 192.168.1.16
+      - type: FTPClient
+
+    - hostname: backup_server
+      type: server
+      ip_address: 192.168.1.16
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.1.1
+      dns_server: 192.168.1.10
+      services:
+      - type: FTPServer
+
+    - hostname: security_suite
+      type: server
+      ip_address: 192.168.1.110
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.1.1
+      dns_server: 192.168.1.10
+      network_interfaces:
+        2: # unfortunately this number is currently meaningless, they're just added in order and take up the next available slot
+          ip_address: 192.168.10.110
+          subnet_mask: 255.255.255.0
+
+    - hostname: client_1
+      type: computer
+      ip_address: 192.168.10.21
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.10.1
+      dns_server: 192.168.1.10
+      applications:
+      - type: DataManipulationBot
+        options:
+          port_scan_p_of_success: 0.8
+          data_manipulation_p_of_success: 0.8
+          payload: "DELETE"
+          server_ip: 192.168.1.14
+      - type: WebBrowser
+        options:
+          target_url: http://arcd.com/users/
+      - type: DatabaseClient
+        options:
+          db_server_ip: 192.168.1.14
+      services:
+      - type: DNSClient
+
+    - hostname: client_2
+      type: computer
+      ip_address: 192.168.10.22
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.10.1
+      dns_server: 192.168.1.10
+      applications:
+      - type: WebBrowser
+        options:
+          target_url: http://arcd.com/users/
+      - type: DataManipulationBot
+        options:
+          port_scan_p_of_success: 0.8
+          data_manipulation_p_of_success: 0.8
+          payload: "DELETE"
+          server_ip: 192.168.1.14
+      - type: DatabaseClient
+        options:
+          db_server_ip: 192.168.1.14
+      services:
+      - type: DNSClient
+
+
+
+    links:
+    - endpoint_a_hostname: router_1
+      endpoint_a_port: 1
+      endpoint_b_hostname: switch_1
+      endpoint_b_port: 8
+    - endpoint_a_hostname: router_1
+      endpoint_a_port: 2
+      endpoint_b_hostname: switch_2
+      endpoint_b_port: 8
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 1
+      endpoint_b_hostname: domain_controller
+      endpoint_b_port: 1
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 2
+      endpoint_b_hostname: web_server
+      endpoint_b_port: 1
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 3
+      endpoint_b_hostname: database_server
+      endpoint_b_port: 1
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 4
+      endpoint_b_hostname: backup_server
+      endpoint_b_port: 1
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 7
+      endpoint_b_hostname: security_suite
+      endpoint_b_port: 1
+    - endpoint_a_hostname: switch_2
+      endpoint_a_port: 1
+      endpoint_b_hostname: client_1
+      endpoint_b_port: 1
+    - endpoint_a_hostname: switch_2
+      endpoint_a_port: 2
+      endpoint_b_hostname: client_2
+      endpoint_b_port: 1
+    - endpoint_a_hostname: switch_2
+      endpoint_a_port: 7
+      endpoint_b_hostname: security_suite
+      endpoint_b_port: 2
--- a/tests/assets/configs/fix_duration_one_item.yaml
+++ b/tests/assets/configs/fix_duration_one_item.yaml
@@ -0,0 +1,248 @@
+#  Basic Switched network
+#
+#  --------------      --------------      --------------
+#  |  client_1  |------|  switch_1  |------|  client_2  |
+#  --------------      --------------      --------------
+#
+io_settings:
+  save_step_metadata: false
+  save_pcap_logs: true
+  save_sys_logs: true
+  sys_log_level: WARNING
+
+
+game:
+  max_episode_length: 256
+  ports:
+  - ARP
+  - DNS
+  - HTTP
+  - POSTGRES_SERVER
+  protocols:
+  - ICMP
+  - TCP
+  - UDP
+
+agents:
+  - ref: client_2_green_user
+    team: GREEN
+    type: ProbabilisticAgent
+    observation_space: null
+    action_space:
+      action_list:
+        - type: DONOTHING
+        - type: NODE_APPLICATION_EXECUTE
+      action_map:
+        0:
+          action: DONOTHING
+          options: {}
+        1:
+          action: NODE_APPLICATION_EXECUTE
+          options:
+            node_id: 0
+            application_id: 0
+      options:
+        nodes:
+        - node_name: client_2
+          applications:
+            - application_name: WebBrowser
+        max_folders_per_node: 1
+        max_files_per_folder: 1
+        max_services_per_node: 1
+        max_applications_per_node: 1
+
+    reward_function:
+      reward_components:
+        - type: DUMMY
+
+    agent_settings:
+      start_settings:
+        start_step: 5
+        frequency: 4
+        variance: 3
+
+
+
+  - ref: defender
+    team: BLUE
+    type: ProxyAgent
+
+    observation_space:
+      type: CUSTOM
+      options:
+        components:
+          - type: NODES
+            label: NODES
+            options:
+              hosts:
+                - hostname: client_1
+                - hostname: client_2
+                - hostname: client_3
+              num_services: 1
+              num_applications: 0
+              num_folders: 1
+              num_files: 1
+              num_nics: 2
+              include_num_access: false
+              monitored_traffic:
+                icmp:
+                    - NONE
+                tcp:
+                    - DNS
+              include_nmne: true
+              routers:
+                - hostname: router_1
+              num_ports: 0
+              ip_list:
+                - 192.168.10.21
+                - 192.168.10.22
+                - 192.168.10.23
+              wildcard_list:
+                - 0.0.0.1
+              port_list:
+                - 80
+                - 5432
+              protocol_list:
+                - ICMP
+                - TCP
+                - UDP
+              num_rules: 10
+
+          - type: LINKS
+            label: LINKS
+            options:
+              link_references:
+                - switch_1:eth-1<->client_1:eth-1
+                - switch_1:eth-2<->client_2:eth-1
+          - type: "NONE"
+            label: ICS
+            options: {}
+
+    action_space:
+      action_list:
+        - type: DONOTHING
+
+      action_map:
+          0:
+            action: DONOTHING
+            options: {}
+      options:
+        nodes:
+        - node_name: switch
+        - node_name: client_1
+        - node_name: client_2
+        - node_name: client_3
+        max_folders_per_node: 2
+        max_files_per_folder: 2
+        max_services_per_node: 2
+        max_nics_per_node: 8
+        max_acl_rules: 10
+        ip_list:
+          - 192.168.10.21
+          - 192.168.10.22
+          - 192.168.10.23
+
+    reward_function:
+      reward_components:
+        - type: DATABASE_FILE_INTEGRITY
+          weight: 0.5
+          options:
+            node_hostname: database_server
+            folder_name: database
+            file_name: database.db
+
+
+        - type: WEB_SERVER_404_PENALTY
+          weight: 0.5
+          options:
+            node_hostname: web_server
+            service_name: web_server_web_service
+
+
+    agent_settings:
+      flatten_obs: true
+
+simulation:
+  network:
+    nodes:
+
+    - type: switch
+      hostname: switch_1
+      num_ports: 8
+
+    - hostname: client_1
+      type: computer
+      ip_address: 192.168.10.21
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.10.1
+      dns_server: 192.168.1.10
+      applications:
+      - type: RansomwareScript
+      - type: WebBrowser
+        options:
+          target_url: http://arcd.com/users/
+      - type: DatabaseClient
+        options:
+          db_server_ip: 192.168.1.10
+          server_password: arcd
+          fix_duration: 1
+      - type: DataManipulationBot
+        options:
+          port_scan_p_of_success: 0.8
+          data_manipulation_p_of_success: 0.8
+          payload: "DELETE"
+          server_ip: 192.168.1.21
+          server_password: arcd
+      - type: DoSBot
+        options:
+          target_ip_address: 192.168.10.21
+          payload: SPOOF DATA
+          port_scan_p_of_success: 0.8
+      services:
+      - type: DNSClient
+        options:
+          dns_server: 192.168.1.10
+      - type: DNSServer
+        options:
+          domain_mapping:
+            arcd.com: 192.168.1.10
+      - type: DatabaseService
+        options:
+          fix_duration: 5
+          backup_server_ip: 192.168.1.10
+      - type: WebServer
+      - type: FTPClient
+      - type: FTPServer
+        options:
+          server_password: arcd
+      - type: NTPClient
+        options:
+          ntp_server_ip: 192.168.1.10
+      - type: NTPServer
+    - hostname: client_2
+      type: computer
+      ip_address: 192.168.10.22
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.10.1
+      dns_server: 192.168.1.10
+      applications:
+        - type: DatabaseClient
+          options:
+            db_server_ip: 192.168.1.10
+            server_password: arcd
+      services:
+        - type: DNSClient
+          options:
+            dns_server: 192.168.1.10
+
+    links:
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 1
+      endpoint_b_hostname: client_1
+      endpoint_b_port: 1
+      bandwidth: 200
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 2
+      endpoint_b_hostname: client_2
+      endpoint_b_port: 1
+      bandwidth: 200
--- a/tests/assets/configs/install_and_configure_apps.yaml
+++ b/tests/assets/configs/install_and_configure_apps.yaml
@@ -0,0 +1,142 @@
+io_settings:
+  save_step_metadata: false
+  save_pcap_logs: false
+  save_sys_logs: false
+  save_agent_actions: false
+
+game:
+  max_episode_length: 256
+  ports:
+    - ARP
+    - DNS
+  protocols:
+    - ICMP
+    - TCP
+
+agents:
+  - ref: agent_1
+    team: BLUE
+    type: ProxyAgent
+
+    observation_space: null
+    action_space:
+      action_list:
+        - type: DONOTHING
+        - type: NODE_APPLICATION_INSTALL
+        - type: CONFIGURE_DATABASE_CLIENT
+        - type: CONFIGURE_DOSBOT
+        - type: CONFIGURE_RANSOMWARE_SCRIPT
+        - type: NODE_APPLICATION_REMOVE
+      action_map:
+        0:
+          action: DONOTHING
+          options: {}
+        1:
+          action: NODE_APPLICATION_INSTALL
+          options:
+            node_id: 0
+            application_name: DatabaseClient
+        2:
+          action: NODE_APPLICATION_INSTALL
+          options:
+            node_id: 1
+            application_name: RansomwareScript
+        3:
+          action: NODE_APPLICATION_INSTALL
+          options:
+            node_id: 2
+            application_name: DoSBot
+        4:
+          action: CONFIGURE_DATABASE_CLIENT
+          options:
+            node_id: 0
+            config:
+              server_ip_address: 10.0.0.5
+        5:
+          action: CONFIGURE_DATABASE_CLIENT
+          options:
+            node_id: 0
+            config:
+              server_password: correct_password
+        6:
+          action: CONFIGURE_RANSOMWARE_SCRIPT
+          options:
+            node_id: 1
+            config:
+              server_ip_address: 10.0.0.5
+              server_password: correct_password
+              payload: ENCRYPT
+        7:
+          action: CONFIGURE_DOSBOT
+          options:
+            node_id: 2
+            config:
+              target_ip_address: 10.0.0.5
+              target_port: POSTGRES_SERVER
+              payload: DELETE
+              repeat: true
+              port_scan_p_of_success: 1.0
+              dos_intensity: 1.0
+              max_sessions: 1000
+        8:
+          action: NODE_APPLICATION_INSTALL
+          options:
+            node_id: 1
+            application_name: DatabaseClient
+      options:
+        nodes:
+          - node_name: client_1
+          - node_name: client_2
+          - node_name: client_3
+        ip_list: []
+    reward_function:
+      reward_components:
+        - type: DUMMY
+
+simulation:
+  network:
+    nodes:
+      - type: computer
+        hostname: client_1
+        ip_address: 10.0.0.2
+        subnet_mask: 255.255.255.0
+        default_gateway: 10.0.0.1
+      - type: computer
+        hostname: client_2
+        ip_address: 10.0.0.3
+        subnet_mask: 255.255.255.0
+        default_gateway: 10.0.0.1
+      - type: computer
+        hostname: client_3
+        ip_address: 10.0.0.4
+        subnet_mask: 255.255.255.0
+        default_gateway: 10.0.0.1
+      - type: switch
+        hostname: switch_1
+        num_ports: 8
+      - type: server
+        hostname: server_1
+        ip_address: 10.0.0.5
+        subnet_mask: 255.255.255.0
+        default_gateway: 10.0.0.1
+        services:
+          - type: DatabaseService
+            options:
+              db_password: correct_password
+    links:
+      - endpoint_a_hostname: client_1
+        endpoint_a_port: 1
+        endpoint_b_hostname: switch_1
+        endpoint_b_port: 1
+      - endpoint_a_hostname: client_2
+        endpoint_a_port: 1
+        endpoint_b_hostname: switch_1
+        endpoint_b_port: 2
+      - endpoint_a_hostname: client_3
+        endpoint_a_port: 1
+        endpoint_b_hostname: switch_1
+        endpoint_b_port: 3
+      - endpoint_a_hostname: server_1
+        endpoint_a_port: 1
+        endpoint_b_hostname: switch_1
+        endpoint_b_port: 8
--- a/tests/assets/configs/software_fix_duration.yaml
+++ b/tests/assets/configs/software_fix_duration.yaml
@@ -0,0 +1,263 @@
+#  Basic Switched network
+#
+#  --------------      --------------      --------------
+#  |  client_1  |------|  switch_1  |------|  client_2  |
+#  --------------      --------------      --------------
+#
+io_settings:
+  save_step_metadata: false
+  save_pcap_logs: true
+  save_sys_logs: true
+  sys_log_level: WARNING
+
+
+game:
+  max_episode_length: 256
+  ports:
+  - ARP
+  - DNS
+  - HTTP
+  - POSTGRES_SERVER
+  protocols:
+  - ICMP
+  - TCP
+  - UDP
+
+agents:
+  - ref: client_2_green_user
+    team: GREEN
+    type: ProbabilisticAgent
+    observation_space: null
+    action_space:
+      action_list:
+        - type: DONOTHING
+        - type: NODE_APPLICATION_EXECUTE
+      action_map:
+        0:
+          action: DONOTHING
+          options: {}
+        1:
+          action: NODE_APPLICATION_EXECUTE
+          options:
+            node_id: 0
+            application_id: 0
+      options:
+        nodes:
+        - node_name: client_2
+          applications:
+            - application_name: WebBrowser
+        max_folders_per_node: 1
+        max_files_per_folder: 1
+        max_services_per_node: 1
+        max_applications_per_node: 1
+
+    reward_function:
+      reward_components:
+        - type: DUMMY
+
+    agent_settings:
+      start_settings:
+        start_step: 5
+        frequency: 4
+        variance: 3
+
+
+
+  - ref: defender
+    team: BLUE
+    type: ProxyAgent
+
+    observation_space:
+      type: CUSTOM
+      options:
+        components:
+          - type: NODES
+            label: NODES
+            options:
+              hosts:
+                - hostname: client_1
+                - hostname: client_2
+                - hostname: client_3
+              num_services: 1
+              num_applications: 0
+              num_folders: 1
+              num_files: 1
+              num_nics: 2
+              include_num_access: false
+              monitored_traffic:
+                icmp:
+                    - NONE
+                tcp:
+                    - DNS
+              include_nmne: true
+              routers:
+                - hostname: router_1
+              num_ports: 0
+              ip_list:
+                - 192.168.10.21
+                - 192.168.10.22
+                - 192.168.10.23
+              wildcard_list:
+                - 0.0.0.1
+              port_list:
+                - 80
+                - 5432
+              protocol_list:
+                - ICMP
+                - TCP
+                - UDP
+              num_rules: 10
+
+          - type: LINKS
+            label: LINKS
+            options:
+              link_references:
+                - switch_1:eth-1<->client_1:eth-1
+                - switch_1:eth-2<->client_2:eth-1
+          - type: "NONE"
+            label: ICS
+            options: {}
+
+    action_space:
+      action_list:
+        - type: DONOTHING
+
+      action_map:
+          0:
+            action: DONOTHING
+            options: {}
+      options:
+        nodes:
+        - node_name: switch
+        - node_name: client_1
+        - node_name: client_2
+        - node_name: client_3
+        max_folders_per_node: 2
+        max_files_per_folder: 2
+        max_services_per_node: 2
+        max_nics_per_node: 8
+        max_acl_rules: 10
+        ip_list:
+          - 192.168.10.21
+          - 192.168.10.22
+          - 192.168.10.23
+
+    reward_function:
+      reward_components:
+        - type: DATABASE_FILE_INTEGRITY
+          weight: 0.5
+          options:
+            node_hostname: database_server
+            folder_name: database
+            file_name: database.db
+
+
+        - type: WEB_SERVER_404_PENALTY
+          weight: 0.5
+          options:
+            node_hostname: web_server
+            service_name: web_server_web_service
+
+
+    agent_settings:
+      flatten_obs: true
+
+simulation:
+  network:
+    nodes:
+
+    - type: switch
+      hostname: switch_1
+      num_ports: 8
+
+    - hostname: client_1
+      type: computer
+      ip_address: 192.168.10.21
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.10.1
+      dns_server: 192.168.1.10
+      applications:
+      - type: RansomwareScript
+        options:
+          fix_duration: 1
+      - type: WebBrowser
+        options:
+          target_url: http://arcd.com/users/
+          fix_duration: 1
+      - type: DatabaseClient
+        options:
+          db_server_ip: 192.168.1.10
+          server_password: arcd
+          fix_duration: 1
+      - type: DataManipulationBot
+        options:
+          port_scan_p_of_success: 0.8
+          data_manipulation_p_of_success: 0.8
+          payload: "DELETE"
+          server_ip: 192.168.1.21
+          server_password: arcd
+          fix_duration: 1
+      - type: DoSBot
+        options:
+          target_ip_address: 192.168.10.21
+          payload: SPOOF DATA
+          port_scan_p_of_success: 0.8
+          fix_duration: 1
+      services:
+      - type: DNSClient
+        options:
+          dns_server: 192.168.1.10
+          fix_duration: 3
+      - type: DNSServer
+        options:
+          fix_duration: 3
+          domain_mapping:
+            arcd.com: 192.168.1.10
+      - type: DatabaseService
+        options:
+          backup_server_ip: 192.168.1.10
+          fix_duration: 3
+      - type: WebServer
+        options:
+          fix_duration: 3
+      - type: FTPClient
+        options:
+          fix_duration: 3
+      - type: FTPServer
+        options:
+          server_password: arcd
+          fix_duration: 3
+      - type: NTPClient
+        options:
+          ntp_server_ip: 192.168.1.10
+          fix_duration: 3
+      - type: NTPServer
+        options:
+          fix_duration: 3
+    - hostname: client_2
+      type: computer
+      ip_address: 192.168.10.22
+      subnet_mask: 255.255.255.0
+      default_gateway: 192.168.10.1
+      dns_server: 192.168.1.10
+      applications:
+        - type: DatabaseClient
+          options:
+            db_server_ip: 192.168.1.10
+            server_password: arcd
+      services:
+        - type: DNSClient
+          options:
+            dns_server: 192.168.1.10
+
+    links:
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 1
+      endpoint_b_hostname: client_1
+      endpoint_b_port: 1
+      bandwidth: 200
+    - endpoint_a_hostname: switch_1
+      endpoint_a_port: 2
+      endpoint_b_hostname: client_2
+      endpoint_b_port: 1
+      bandwidth: 200
--- a/tests/assets/configs/test_application_install.yaml
+++ b/tests/assets/configs/test_application_install.yaml
@@ -260,6 +260,7 @@ agents:
        - type: NODE_APPLICATION_INSTALL
        - type: NODE_APPLICATION_REMOVE
        - type: NODE_APPLICATION_EXECUTE
+        - type: CONFIGURE_DOSBOT

      action_map:
          0:
@@ -683,7 +684,6 @@ agents:
            options:
              node_id: 0
              application_name: DoSBot
-              ip_address: 192.168.1.14
          79:
            action: NODE_APPLICATION_REMOVE
            options:
@@ -699,6 +699,14 @@ agents:
            options:
              node_id: 0
              application_id: 0
+          82:
+            action: CONFIGURE_DOSBOT
+            options:
+              node_id: 0
+              config:
+                target_ip_address: 192.168.1.14
+                target_port: POSTGRES_SERVER
+



--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -51,11 +51,11 @@ class TestService(Service):
        pass


-class TestApplication(Application):
+class DummyApplication(Application, identifier="DummyApplication"):
    """Test Application class"""

    def __init__(self, **kwargs):
-        kwargs["name"] = "TestApplication"
+        kwargs["name"] = "DummyApplication"
        kwargs["port"] = Port.HTTP
        kwargs["protocol"] = IPProtocol.TCP
        super().__init__(**kwargs)
@@ -85,15 +85,15 @@ def service_class():


@pytest.fixture(scope="function")
-def application(file_system) -> TestApplication:
-    return TestApplication(
-        name="TestApplication", port=Port.ARP, file_system=file_system, sys_log=SysLog(hostname="test_application")
+def application(file_system) -> DummyApplication:
+    return DummyApplication(
+        name="DummyApplication", port=Port.ARP, file_system=file_system, sys_log=SysLog(hostname="dummy_application")
    )


@pytest.fixture(scope="function")
 def application_class():
-    return TestApplication
+    return DummyApplication


@pytest.fixture(scope="function")
--- a/tests/e2e_integration_tests/test_uc2_data_manipulation_scenario.py
+++ b/tests/e2e_integration_tests/test_uc2_data_manipulation_scenario.py
@@ -69,6 +69,7 @@ def test_application_install_uninstall_on_uc2():
    env.step(0)

    # Test we can now execute the DoSBot app
+    env.step(82)  # configure dos bot with ip address and port
    _, _, _, _, info = env.step(81)
    assert info["agent_actions"]["defender"].response.status == "success"

--- a/tests/integration_tests/configuration_file_parsing/software_installation_and_configuration.py
+++ b/tests/integration_tests/configuration_file_parsing/software_installation_and_configuration.py
@@ -9,9 +9,10 @@ from primaite.config.load import data_manipulation_config_path
 from primaite.game.agent.interface import ProxyAgent
 from primaite.game.agent.scripted_agents.data_manipulation_bot import DataManipulationAgent
 from primaite.game.agent.scripted_agents.probabilistic_agent import ProbabilisticAgent
-from primaite.game.game import APPLICATION_TYPES_MAPPING, PrimaiteGame, SERVICE_TYPES_MAPPING
+from primaite.game.game import PrimaiteGame, SERVICE_TYPES_MAPPING
 from primaite.simulator.network.container import Network
 from primaite.simulator.network.hardware.nodes.host.computer import Computer
+from primaite.simulator.system.applications.application import Application
 from primaite.simulator.system.applications.database_client import DatabaseClient
 from primaite.simulator.system.applications.red_applications.data_manipulation_bot import DataManipulationBot
 from primaite.simulator.system.applications.red_applications.dos_bot import DoSBot
@@ -85,7 +86,7 @@ def test_node_software_install():
        assert client_2.software_manager.software.get(software.__name__) is not None

    # check that applications have been installed on client 1
-    for applications in APPLICATION_TYPES_MAPPING:
+    for applications in Application._application_registry:
        assert client_1.software_manager.software.get(applications) is not None

    # check that services have been installed on client 1
--- a/tests/integration_tests/configuration_file_parsing/test_software_fix_duration.py
+++ b/tests/integration_tests/configuration_file_parsing/test_software_fix_duration.py
@@ -0,0 +1,93 @@
+# © Crown-owned copyright 2024, Defence Science and Technology Laboratory UK
+import copy
+from ipaddress import IPv4Address
+from pathlib import Path
+from typing import Union
+
+import yaml
+
+from primaite.config.load import data_manipulation_config_path
+from primaite.game.agent.interface import ProxyAgent
+from primaite.game.agent.scripted_agents.data_manipulation_bot import DataManipulationAgent
+from primaite.game.agent.scripted_agents.probabilistic_agent import ProbabilisticAgent
+from primaite.game.game import APPLICATION_TYPES_MAPPING, PrimaiteGame, SERVICE_TYPES_MAPPING
+from primaite.simulator.network.container import Network
+from primaite.simulator.network.hardware.nodes.host.computer import Computer
+from primaite.simulator.system.applications.database_client import DatabaseClient
+from primaite.simulator.system.applications.red_applications.data_manipulation_bot import DataManipulationBot
+from primaite.simulator.system.applications.red_applications.dos_bot import DoSBot
+from primaite.simulator.system.applications.web_browser import WebBrowser
+from primaite.simulator.system.services.database.database_service import DatabaseService
+from primaite.simulator.system.services.dns.dns_client import DNSClient
+from primaite.simulator.system.services.dns.dns_server import DNSServer
+from primaite.simulator.system.services.ftp.ftp_client import FTPClient
+from primaite.simulator.system.services.ftp.ftp_server import FTPServer
+from primaite.simulator.system.services.ntp.ntp_client import NTPClient
+from primaite.simulator.system.services.ntp.ntp_server import NTPServer
+from primaite.simulator.system.services.web_server.web_server import WebServer
+from tests import TEST_ASSETS_ROOT
+
+TEST_CONFIG = TEST_ASSETS_ROOT / "configs/software_fix_duration.yaml"
+ONE_ITEM_CONFIG = TEST_ASSETS_ROOT / "configs/fix_duration_one_item.yaml"
+
+
+def load_config(config_path: Union[str, Path]) -> PrimaiteGame:
+    """Returns a PrimaiteGame object which loads the contents of a given yaml path."""
+    with open(config_path, "r") as f:
+        cfg = yaml.safe_load(f)
+
+    return PrimaiteGame.from_config(cfg)
+
+
+def test_default_fix_duration():
+    """Test that software with no defined fix duration in config uses the default fix duration of 2."""
+    game = load_config(TEST_CONFIG)
+    client_2: Computer = game.simulation.network.get_node_by_hostname("client_2")
+
+    database_client: DatabaseClient = client_2.software_manager.software.get("DatabaseClient")
+    assert database_client.fixing_duration == 2
+
+    dns_client: DNSClient = client_2.software_manager.software.get("DNSClient")
+    assert dns_client.fixing_duration == 2
+
+
+def test_fix_duration_set_from_config():
+    """Test to check that the fix duration set for applications and services works as intended."""
+    game = load_config(TEST_CONFIG)
+    client_1: Computer = game.simulation.network.get_node_by_hostname("client_1")
+
+    # in config - services take 3 timesteps to fix
+    for service in SERVICE_TYPES_MAPPING:
+        assert client_1.software_manager.software.get(service) is not None
+        assert client_1.software_manager.software.get(service).fixing_duration == 3
+
+    # in config - applications take 1 timestep to fix
+    for applications in APPLICATION_TYPES_MAPPING:
+        assert client_1.software_manager.software.get(applications) is not None
+        assert client_1.software_manager.software.get(applications).fixing_duration == 1
+
+
+def test_fix_duration_for_one_item():
+    """Test that setting fix duration for one application does not affect other components."""
+    game = load_config(ONE_ITEM_CONFIG)
+    client_1: Computer = game.simulation.network.get_node_by_hostname("client_1")
+
+    # in config - services take 3 timesteps to fix
+    services = copy.copy(SERVICE_TYPES_MAPPING)
+    services.pop("DatabaseService")
+    for service in services:
+        assert client_1.software_manager.software.get(service) is not None
+        assert client_1.software_manager.software.get(service).fixing_duration == 2
+
+    # in config - applications take 1 timestep to fix
+    applications = copy.copy(APPLICATION_TYPES_MAPPING)
+    applications.pop("DatabaseClient")
+    for applications in applications:
+        assert client_1.software_manager.software.get(applications) is not None
+        assert client_1.software_manager.software.get(applications).fixing_duration == 2
+
+    database_client: DatabaseClient = client_1.software_manager.software.get("DatabaseClient")
+    assert database_client.fixing_duration == 1
+
+    database_service: DatabaseService = client_1.software_manager.software.get("DatabaseService")
+    assert database_service.fixing_duration == 5
--- a/tests/integration_tests/game_layer/actions/init.py
+++ b/tests/integration_tests/game_layer/actions/init.py
@@ -0,0 +1 @@
+# © Crown-owned copyright 2024, Defence Science and Technology Laboratory UK
--- a/tests/integration_tests/game_layer/actions/test_configure_actions.py
+++ b/tests/integration_tests/game_layer/actions/test_configure_actions.py
@@ -0,0 +1,292 @@
+# © Crown-owned copyright 2024, Defence Science and Technology Laboratory UK
+from ipaddress import IPv4Address
+
+import pytest
+from pydantic import ValidationError
+
+from primaite.game.agent.actions import (
+    ConfigureDatabaseClientAction,
+    ConfigureDoSBotAction,
+    ConfigureRansomwareScriptAction,
+)
+from primaite.session.environment import PrimaiteGymEnv
+from primaite.simulator.file_system.file_system_item_abc import FileSystemItemHealthStatus
+from primaite.simulator.network.transmission.transport_layer import Port
+from primaite.simulator.system.applications.application import ApplicationOperatingState
+from primaite.simulator.system.applications.database_client import DatabaseClient
+from primaite.simulator.system.applications.red_applications.dos_bot import DoSBot
+from primaite.simulator.system.applications.red_applications.ransomware_script import RansomwareScript
+from primaite.simulator.system.services.database.database_service import DatabaseService
+from tests import TEST_ASSETS_ROOT
+from tests.conftest import ControlledAgent
+
+APP_CONFIG_YAML = TEST_ASSETS_ROOT / "configs/install_and_configure_apps.yaml"
+
+
+class TestConfigureDatabaseAction:
+    def test_configure_ip_password(self, game_and_agent):
+        game, agent = game_and_agent
+        agent: ControlledAgent
+        agent.action_manager.actions["CONFIGURE_DATABASE_CLIENT"] = ConfigureDatabaseClientAction(agent.action_manager)
+
+        # make sure there is a database client on this node
+        client_1 = game.simulation.network.get_node_by_hostname("client_1")
+        client_1.software_manager.install(DatabaseClient)
+        db_client: DatabaseClient = client_1.software_manager.software["DatabaseClient"]
+
+        action = (
+            "CONFIGURE_DATABASE_CLIENT",
+            {
+                "node_id": 0,
+                "config": {
+                    "server_ip_address": "192.168.1.99",
+                    "server_password": "admin123",
+                },
+            },
+        )
+        agent.store_action(action)
+        game.step()
+
+        assert db_client.server_ip_address == IPv4Address("192.168.1.99")
+        assert db_client.server_password == "admin123"
+
+    def test_configure_ip(self, game_and_agent):
+        game, agent = game_and_agent
+        agent: ControlledAgent
+        agent.action_manager.actions["CONFIGURE_DATABASE_CLIENT"] = ConfigureDatabaseClientAction(agent.action_manager)
+
+        # make sure there is a database client on this node
+        client_1 = game.simulation.network.get_node_by_hostname("client_1")
+        client_1.software_manager.install(DatabaseClient)
+        db_client: DatabaseClient = client_1.software_manager.software["DatabaseClient"]
+
+        action = (
+            "CONFIGURE_DATABASE_CLIENT",
+            {
+                "node_id": 0,
+                "config": {
+                    "server_ip_address": "192.168.1.99",
+                },
+            },
+        )
+        agent.store_action(action)
+        game.step()
+
+        assert db_client.server_ip_address == IPv4Address("192.168.1.99")
+        assert db_client.server_password is None
+
+    def test_configure_password(self, game_and_agent):
+        game, agent = game_and_agent
+        agent: ControlledAgent
+        agent.action_manager.actions["CONFIGURE_DATABASE_CLIENT"] = ConfigureDatabaseClientAction(agent.action_manager)
+
+        # make sure there is a database client on this node
+        client_1 = game.simulation.network.get_node_by_hostname("client_1")
+        client_1.software_manager.install(DatabaseClient)
+        db_client: DatabaseClient = client_1.software_manager.software["DatabaseClient"]
+        old_ip = db_client.server_ip_address
+
+        action = (
+            "CONFIGURE_DATABASE_CLIENT",
+            {
+                "node_id": 0,
+                "config": {
+                    "server_password": "admin123",
+                },
+            },
+        )
+        agent.store_action(action)
+        game.step()
+
+        assert db_client.server_ip_address == old_ip
+        assert db_client.server_password is "admin123"
+
+
+class TestConfigureRansomwareScriptAction:
+    @pytest.mark.parametrize(
+        "config",
+        [
+            {},
+            {"server_ip_address": "181.181.181.181"},
+            {"server_password": "admin123"},
+            {"payload": "ENCRYPT"},
+            {
+                "server_ip_address": "181.181.181.181",
+                "server_password": "admin123",
+                "payload": "ENCRYPT",
+            },
+        ],
+    )
+    def test_configure_ip_password(self, game_and_agent, config):
+        game, agent = game_and_agent
+        agent: ControlledAgent
+        agent.action_manager.actions["CONFIGURE_RANSOMWARE_SCRIPT"] = ConfigureRansomwareScriptAction(
+            agent.action_manager
+        )
+
+        # make sure there is a database client on this node
+        client_1 = game.simulation.network.get_node_by_hostname("client_1")
+        client_1.software_manager.install(RansomwareScript)
+        ransomware_script: RansomwareScript = client_1.software_manager.software["RansomwareScript"]
+
+        old_ip = ransomware_script.server_ip_address
+        old_pw = ransomware_script.server_password
+        old_payload = ransomware_script.payload
+
+        action = (
+            "CONFIGURE_RANSOMWARE_SCRIPT",
+            {"node_id": 0, "config": config},
+        )
+        agent.store_action(action)
+        game.step()
+
+        expected_ip = old_ip if "server_ip_address" not in config else IPv4Address(config["server_ip_address"])
+        expected_pw = old_pw if "server_password" not in config else config["server_password"]
+        expected_payload = old_payload if "payload" not in config else config["payload"]
+
+        assert ransomware_script.server_ip_address == expected_ip
+        assert ransomware_script.server_password == expected_pw
+        assert ransomware_script.payload == expected_payload
+
+    def test_invalid_config(self, game_and_agent):
+        game, agent = game_and_agent
+        agent: ControlledAgent
+        agent.action_manager.actions["CONFIGURE_RANSOMWARE_SCRIPT"] = ConfigureRansomwareScriptAction(
+            agent.action_manager
+        )
+
+        # make sure there is a database client on this node
+        client_1 = game.simulation.network.get_node_by_hostname("client_1")
+        client_1.software_manager.install(RansomwareScript)
+        ransomware_script: RansomwareScript = client_1.software_manager.software["RansomwareScript"]
+        action = (
+            "CONFIGURE_RANSOMWARE_SCRIPT",
+            {
+                "node_id": 0,
+                "config": {"server_password": "admin123", "bad_option": 70},
+            },
+        )
+        agent.store_action(action)
+        with pytest.raises(ValidationError):
+            game.step()
+
+
+class TestConfigureDoSBot:
+    def test_configure_DoSBot(self, game_and_agent):
+        game, agent = game_and_agent
+        agent: ControlledAgent
+        agent.action_manager.actions["CONFIGURE_DOSBOT"] = ConfigureDoSBotAction(agent.action_manager)
+
+        client_1 = game.simulation.network.get_node_by_hostname("client_1")
+        client_1.software_manager.install(DoSBot)
+        dos_bot: DoSBot = client_1.software_manager.software["DoSBot"]
+
+        action = (
+            "CONFIGURE_DOSBOT",
+            {
+                "node_id": 0,
+                "config": {
+                    "target_ip_address": "192.168.1.99",
+                    "target_port": "POSTGRES_SERVER",
+                    "payload": "HACC",
+                    "repeat": False,
+                    "port_scan_p_of_success": 0.875,
+                    "dos_intensity": 0.75,
+                    "max_sessions": 50,
+                },
+            },
+        )
+        agent.store_action(action)
+        game.step()
+
+        assert dos_bot.target_ip_address == IPv4Address("192.168.1.99")
+        assert dos_bot.target_port == Port.POSTGRES_SERVER
+        assert dos_bot.payload == "HACC"
+        assert not dos_bot.repeat
+        assert dos_bot.port_scan_p_of_success == 0.875
+        assert dos_bot.dos_intensity == 0.75
+        assert dos_bot.max_sessions == 50
+
+
+class TestConfigureYAML:
+    def test_configure_db_client(self):
+        env = PrimaiteGymEnv(env_config=APP_CONFIG_YAML)
+
+        # make sure there's no db client on the node yet
+        client_1 = env.game.simulation.network.get_node_by_hostname("client_1")
+        assert client_1.software_manager.software.get("DatabaseClient") is None
+
+        # take the install action, check that the db gets installed, step to get it to finish installing
+        env.step(1)
+        db_client: DatabaseClient = client_1.software_manager.software.get("DatabaseClient")
+        assert isinstance(db_client, DatabaseClient)
+        assert db_client.operating_state == ApplicationOperatingState.INSTALLING
+        env.step(0)
+        env.step(0)
+        env.step(0)
+        env.step(0)
+
+        # configure the ip address and check that it changes, but password doesn't change
+        assert db_client.server_ip_address is None
+        assert db_client.server_password is None
+        env.step(4)
+        assert db_client.server_ip_address == IPv4Address("10.0.0.5")
+        assert db_client.server_password is None
+
+        # configure the password and check that it changes, make sure this lets us connect to the db
+        assert not db_client.connect()
+        env.step(5)
+        assert db_client.server_password == "correct_password"
+        assert db_client.connect()
+
+    def test_configure_ransomware_script(self):
+        env = PrimaiteGymEnv(env_config=APP_CONFIG_YAML)
+        client_2 = env.game.simulation.network.get_node_by_hostname("client_2")
+        assert client_2.software_manager.software.get("RansomwareScript") is None
+
+        # install ransomware script
+        env.step(2)
+        ransom = client_2.software_manager.software.get("RansomwareScript")
+        assert isinstance(ransom, RansomwareScript)
+        assert ransom.operating_state == ApplicationOperatingState.INSTALLING
+        env.step(0)
+        env.step(0)
+        env.step(0)
+        env.step(0)
+
+        # make sure it's not working yet because it's not configured and there's no db client
+        assert not ransom.attack()
+        env.step(8)  # install db client on the same node
+        env.step(0)
+        env.step(0)
+        env.step(0)
+        env.step(0)  # let it finish installing
+        assert not ransom.attack()
+
+        # finally, configure the ransomware script with ip and password
+        env.step(6)
+        assert ransom.attack()
+
+        db_server = env.game.simulation.network.get_node_by_hostname("server_1")
+        db_service: DatabaseService = db_server.software_manager.software.get("DatabaseService")
+        assert db_service.db_file.health_status == FileSystemItemHealthStatus.CORRUPT
+
+    def test_configure_dos_bot(self):
+        env = PrimaiteGymEnv(env_config=APP_CONFIG_YAML)
+        client_3 = env.game.simulation.network.get_node_by_hostname("client_3")
+        assert client_3.software_manager.software.get("DoSBot") is None
+
+        # install DoSBot
+        env.step(3)
+        bot = client_3.software_manager.software.get("DoSBot")
+        assert isinstance(bot, DoSBot)
+        assert bot.operating_state == ApplicationOperatingState.INSTALLING
+        env.step(0)
+        env.step(0)
+        env.step(0)
+        env.step(0)
+
+        # make sure dos bot doesn't work before being configured
+        assert not bot.run()
+        env.step(7)
+        assert bot.run()
--- a/tests/integration_tests/game_layer/test_actions.py
+++ b/tests/integration_tests/game_layer/test_actions.py
@@ -557,7 +557,7 @@ def test_node_application_install_and_uninstall_integration(game_and_agent: Tupl

    assert client_1.software_manager.software.get("DoSBot") is None

-    action = ("NODE_APPLICATION_INSTALL", {"node_id": 0, "application_name": "DoSBot", "ip_address": "192.168.1.14"})
+    action = ("NODE_APPLICATION_INSTALL", {"node_id": 0, "application_name": "DoSBot"})
    agent.store_action(action)
    game.step()

--- a/tests/integration_tests/game_layer/test_rewards.py
+++ b/tests/integration_tests/game_layer/test_rewards.py
@@ -1,9 +1,11 @@
 # © Crown-owned copyright 2024, Defence Science and Technology Laboratory UK
+import pytest
 import yaml

 from primaite.game.agent.interface import AgentHistoryItem
-from primaite.game.agent.rewards import GreenAdminDatabaseUnreachablePenalty, WebpageUnavailablePenalty
+from primaite.game.agent.rewards import ActionPenalty, GreenAdminDatabaseUnreachablePenalty, WebpageUnavailablePenalty
 from primaite.game.game import PrimaiteGame
+from primaite.interface.request import RequestResponse
 from primaite.session.environment import PrimaiteGymEnv
 from primaite.simulator.network.hardware.nodes.host.server import Server
 from primaite.simulator.network.hardware.nodes.network.router import ACLAction, Router
@@ -119,3 +121,77 @@ def test_shared_reward():
        g2_reward = env.game.agents["client_2_green_user"].reward_function.current_reward
        blue_reward = env.game.agents["defender"].reward_function.current_reward
        assert blue_reward == g1_reward + g2_reward
+
+
+def test_action_penalty_loads_from_config():
+    """Test to ensure that action penalty is correctly loaded from config into PrimaiteGymEnv"""
+    CFG_PATH = TEST_ASSETS_ROOT / "configs/action_penalty.yaml"
+    with open(CFG_PATH, "r") as f:
+        cfg = yaml.safe_load(f)
+
+    env = PrimaiteGymEnv(env_config=cfg)
+
+    env.reset()
+    defender = env.game.agents["defender"]
+    act_penalty_obj = None
+    for comp in defender.reward_function.reward_components:
+        if isinstance(comp[0], ActionPenalty):
+            act_penalty_obj = comp[0]
+    if act_penalty_obj is None:
+        pytest.fail("Action penalty reward component was not added to the agent from config.")
+    assert act_penalty_obj.action_penalty == -0.75
+    assert act_penalty_obj.do_nothing_penalty == 0.125
+
+
+def test_action_penalty():
+    """Test that the action penalty is correctly applied when agent performs any action"""
+
+    # Create an ActionPenalty Reward
+    Penalty = ActionPenalty(action_penalty=-0.75, do_nothing_penalty=0.125)
+
+    # Assert that penalty is applied if action isn't DONOTHING
+    reward_value = Penalty.calculate(
+        state={},
+        last_action_response=AgentHistoryItem(
+            timestep=0,
+            action="NODE_APPLICATION_EXECUTE",
+            parameters={"node_id": 0, "application_id": 1},
+            request=["execute"],
+            response=RequestResponse.from_bool(True),
+        ),
+    )
+
+    assert reward_value == -0.75
+
+    # Assert that no penalty applied for a DONOTHING action
+    reward_value = Penalty.calculate(
+        state={},
+        last_action_response=AgentHistoryItem(
+            timestep=0,
+            action="DONOTHING",
+            parameters={},
+            request=["do_nothing"],
+            response=RequestResponse.from_bool(True),
+        ),
+    )
+
+    assert reward_value == 0.125
+
+
+def test_action_penalty_e2e(game_and_agent):
+    """Test that we get the right reward for doing actions to fetch a website."""
+    game, agent = game_and_agent
+    agent: ControlledAgent
+    comp = ActionPenalty(action_penalty=-0.75, do_nothing_penalty=0.125)
+
+    agent.reward_function.register_component(comp, 1.0)
+
+    action = ("DONOTHING", {})
+    agent.store_action(action)
+    game.step()
+    assert agent.reward_function.current_reward == 0.125
+
+    action = ("NODE_FILE_SCAN", {"node_id": 0, "folder_id": 0, "file_id": 0})
+    agent.store_action(action)
+    game.step()
+    assert agent.reward_function.current_reward == -0.75
--- a/tests/integration_tests/network/test_broadcast.py
+++ b/tests/integration_tests/network/test_broadcast.py
@@ -41,7 +41,7 @@ class BroadcastService(Service):
        super().send(payload="broadcast", dest_ip_address=ip_network, dest_port=Port.HTTP, ip_protocol=self.protocol)


-class BroadcastClient(Application):
+class BroadcastClient(Application, identifier="BroadcastClient"):
    """A client application to receive broadcast and unicast messages."""

    payloads_received: List = []
--- a/tests/integration_tests/network/test_multi_lan_internet_example_network.py
+++ b/tests/integration_tests/network/test_multi_lan_internet_example_network.py
@@ -3,9 +3,9 @@ from primaite.simulator.network.hardware.nodes.host.computer import Computer
 from primaite.simulator.network.hardware.nodes.host.server import Server
 from primaite.simulator.network.networks import multi_lan_internet_network_example
 from primaite.simulator.system.applications.database_client import DatabaseClient
+from primaite.simulator.system.applications.web_browser import WebBrowser
 from primaite.simulator.system.services.dns.dns_client import DNSClient
 from primaite.simulator.system.services.ftp.ftp_client import FTPClient
-from src.primaite.simulator.system.applications.web_browser import WebBrowser


 def test_all_with_configured_dns_server_ip_can_resolve_url():
--- a/tests/integration_tests/system/test_application_on_node.py
+++ b/tests/integration_tests/system/test_application_on_node.py
@@ -21,7 +21,7 @@ def populated_node(application_class) -> Tuple[Application, Computer]:
    computer.power_on()
    computer.software_manager.install(application_class)

-    app = computer.software_manager.software.get("TestApplication")
+    app = computer.software_manager.software.get("DummyApplication")
    app.run()

    return app, computer
@@ -39,7 +39,7 @@ def test_application_on_offline_node(application_class):
    )
    computer.software_manager.install(application_class)

-    app: Application = computer.software_manager.software.get("TestApplication")
+    app: Application = computer.software_manager.software.get("DummyApplication")

    computer.power_off()

--- a/tests/integration_tests/system/test_database_on_node.py
+++ b/tests/integration_tests/system/test_database_on_node.py
@@ -14,6 +14,7 @@ from primaite.simulator.system.applications.database_client import DatabaseClien
 from primaite.simulator.system.services.database.database_service import DatabaseService
 from primaite.simulator.system.services.ftp.ftp_server import FTPServer
 from primaite.simulator.system.services.service import ServiceOperatingState
+from primaite.simulator.system.software import SoftwareHealthState


@pytest.fixture(scope="function")
@@ -213,6 +214,110 @@ def test_restore_backup_after_deleting_file_without_updating_scan(uc2_network):
    assert db_service.db_file.visible_health_status == FileSystemItemHealthStatus.GOOD  # now looks good


+def test_database_service_fix(uc2_network):
+    """Test that the software fix applies to database service."""
+    db_server: Server = uc2_network.get_node_by_hostname("database_server")
+    db_service: DatabaseService = db_server.software_manager.software["DatabaseService"]
+
+    assert db_service.backup_database() is True
+
+    # delete database locally
+    db_service.file_system.delete_file(folder_name="database", file_name="database.db")
+
+    # db file is gone, reduced to atoms
+    assert db_service.db_file is None
+
+    db_service.fix()  # fix the database service
+
+    assert db_service.health_state_actual == SoftwareHealthState.FIXING
+
+    # apply timestep until the fix is applied
+    for i in range(db_service.fixing_duration + 1):
+        uc2_network.apply_timestep(i)
+
+    assert db_service.db_file.health_status == FileSystemItemHealthStatus.GOOD
+    assert db_service.health_state_actual == SoftwareHealthState.GOOD
+
+
+def test_database_cannot_be_queried_while_fixing(uc2_network):
+    """Tests that the database service cannot be queried if the service is being fixed."""
+    db_server: Server = uc2_network.get_node_by_hostname("database_server")
+    db_service: DatabaseService = db_server.software_manager.software["DatabaseService"]
+
+    web_server: Server = uc2_network.get_node_by_hostname("web_server")
+    db_client: DatabaseClient = web_server.software_manager.software["DatabaseClient"]
+
+    db_connection: DatabaseClientConnection = db_client.get_new_connection()
+
+    assert db_connection.query(sql="SELECT")
+
+    assert db_service.backup_database() is True
+
+    # delete database locally
+    db_service.file_system.delete_file(folder_name="database", file_name="database.db")
+
+    # db file is gone, reduced to atoms
+    assert db_service.db_file is None
+
+    db_service.fix()  # fix the database service
+    assert db_service.health_state_actual == SoftwareHealthState.FIXING
+
+    # fails to query because database is in FIXING state
+    assert db_connection.query(sql="SELECT") is False
+
+    # apply timestep until the fix is applied
+    for i in range(db_service.fixing_duration + 1):
+        uc2_network.apply_timestep(i)
+
+    assert db_service.health_state_actual == SoftwareHealthState.GOOD
+
+    assert db_service.db_file.health_status == FileSystemItemHealthStatus.GOOD
+
+    assert db_connection.query(sql="SELECT")
+
+
+def test_database_can_create_connection_while_fixing(uc2_network):
+    """Tests that connections cannot be created while the database is being fixed."""
+    db_server: Server = uc2_network.get_node_by_hostname("database_server")
+    db_service: DatabaseService = db_server.software_manager.software["DatabaseService"]
+
+    client_2: Server = uc2_network.get_node_by_hostname("client_2")
+    db_client: DatabaseClient = client_2.software_manager.software["DatabaseClient"]
+
+    db_connection: DatabaseClientConnection = db_client.get_new_connection()
+
+    assert db_connection.query(sql="SELECT")
+
+    assert db_service.backup_database() is True
+
+    # delete database locally
+    db_service.file_system.delete_file(folder_name="database", file_name="database.db")
+
+    # db file is gone, reduced to atoms
+    assert db_service.db_file is None
+
+    db_service.fix()  # fix the database service
+    assert db_service.health_state_actual == SoftwareHealthState.FIXING
+
+    # fails to query because database is in FIXING state
+    assert db_connection.query(sql="SELECT") is False
+
+    # should be able to create a new connection
+    new_db_connection: DatabaseClientConnection = db_client.get_new_connection()
+    assert new_db_connection is not None
+    assert new_db_connection.query(sql="SELECT") is False  # still should fail to query because FIXING
+
+    # apply timestep until the fix is applied
+    for i in range(db_service.fixing_duration + 1):
+        uc2_network.apply_timestep(i)
+
+    assert db_service.health_state_actual == SoftwareHealthState.GOOD
+    assert db_service.db_file.health_status == FileSystemItemHealthStatus.GOOD
+
+    assert db_connection.query(sql="SELECT")
+    assert new_db_connection.query(sql="SELECT")
+
+
 def test_database_client_cannot_query_offline_database_server(uc2_network):
    """Tests DB query across the network returns HTTP status 404 when db server is offline."""
    db_server: Server = uc2_network.get_node_by_hostname("database_server")
--- a/tests/integration_tests/system/test_web_client_server_and_database.py
+++ b/tests/integration_tests/system/test_web_client_server_and_database.py
@@ -16,6 +16,7 @@ from primaite.simulator.system.services.database.database_service import Databas
 from primaite.simulator.system.services.dns.dns_client import DNSClient
 from primaite.simulator.system.services.dns.dns_server import DNSServer
 from primaite.simulator.system.services.web_server.web_server import WebServer
+from primaite.simulator.system.software import SoftwareHealthState


@pytest.fixture(scope="function")
@@ -110,6 +111,29 @@ def test_web_client_requests_users(web_client_web_server_database):
    assert web_browser.get_webpage()


+def test_database_fix_disrupts_web_client(uc2_network):
+    """Tests that the database service being in fixed state disrupts the web client."""
+    computer: Computer = uc2_network.get_node_by_hostname("client_1")
+    db_server: Server = uc2_network.get_node_by_hostname("database_server")
+
+    web_browser: WebBrowser = computer.software_manager.software.get("WebBrowser")
+    database_service: DatabaseService = db_server.software_manager.software.get("DatabaseService")
+
+    # fix the database service
+    database_service.fix()
+
+    assert database_service.health_state_actual == SoftwareHealthState.FIXING
+
+    assert web_browser.get_webpage() is False
+
+    for i in range(database_service.fixing_duration + 1):
+        uc2_network.apply_timestep(i)
+
+    assert database_service.health_state_actual == SoftwareHealthState.GOOD
+
+    assert web_browser.get_webpage()
+
+
 class TestWebBrowserHistory:
    def test_populating_history(self, web_client_web_server_database):
        network, computer, _, _ = web_client_web_server_database
--- a/tests/integration_tests/test_simulation/test_request_response.py
+++ b/tests/integration_tests/test_simulation/test_request_response.py
@@ -13,7 +13,7 @@ from primaite.simulator.network.hardware.node_operating_state import NodeOperati
 from primaite.simulator.network.hardware.nodes.host.host_node import HostNode
 from primaite.simulator.network.hardware.nodes.network.router import ACLAction, Router
 from primaite.simulator.network.transmission.transport_layer import Port
-from tests.conftest import TestApplication, TestService
+from tests.conftest import DummyApplication, TestService


 def test_successful_node_file_system_creation_request(example_network):
@@ -47,14 +47,14 @@ def test_successful_application_requests(example_network):
    net = example_network

    client_1 = net.get_node_by_hostname("client_1")
-    client_1.software_manager.install(TestApplication)
-    client_1.software_manager.software.get("TestApplication").run()
+    client_1.software_manager.install(DummyApplication)
+    client_1.software_manager.software.get("DummyApplication").run()

-    resp_1 = net.apply_request(["node", "client_1", "application", "TestApplication", "scan"])
+    resp_1 = net.apply_request(["node", "client_1", "application", "DummyApplication", "scan"])
    assert resp_1 == RequestResponse(status="success", data={})
-    resp_2 = net.apply_request(["node", "client_1", "application", "TestApplication", "fix"])
+    resp_2 = net.apply_request(["node", "client_1", "application", "DummyApplication", "fix"])
    assert resp_2 == RequestResponse(status="success", data={})
-    resp_3 = net.apply_request(["node", "client_1", "application", "TestApplication", "compromise"])
+    resp_3 = net.apply_request(["node", "client_1", "application", "DummyApplication", "compromise"])
    assert resp_3 == RequestResponse(status="success", data={})


--- a/tests/unit_tests/_primaite/_simulator/_system/_applications/test_application_registry.py
+++ b/tests/unit_tests/_primaite/_simulator/_system/_applications/test_application_registry.py
@@ -0,0 +1,22 @@
+# © Crown-owned copyright 2024, Defence Science and Technology Laboratory UK
+import pytest
+
+from primaite.simulator.system.applications.application import Application
+
+
+def test_adding_to_app_registry():
+    class temp_application(Application, identifier="temp_app"):
+        pass
+
+    assert Application._application_registry["temp_app"] is temp_application
+
+    with pytest.raises(ValueError):
+
+        class another_application(Application, identifier="temp_app"):
+            pass
+
+    # This is kinda evil...
+    # Because pytest doesn't reimport classes from modules, registering this temporary test application will change the
+    # state of the Application registry for all subsequently run tests. So, we have to delete and unregister the class.
+    del temp_application
+    Application._application_registry.pop("temp_app")
				`@@ -0,0 +1 @@`
				`# © Crown-owned copyright 2024, Defence Science and Technology Laboratory UK`