Commit a3bde1fd authored by Duggan, John's avatar Duggan, John
Browse files

Fix NERSC run

parent ebb2545e

pixi.lock

+431 −469

File changed.

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pyproject.toml

+1 −1
Original line number Diff line number Diff line 
[project]

name = "ips-fastran-gui"

version = "0.3.2"

version = "0.4.0"

description = "IPS Fastran GUI Project"

authors = []

readme = "README.md"

src/ips_fastran_gui/app/models/ips_fastran.py

+14 −4
Original line number Diff line number Diff line
@@ -3,9 +3,9 @@ 
import logging

import os

import zipfile

from typing import List, Tuple

from typing import Callable, List, Tuple



from nova.galaxy import Dataset, Parameters, Tool

from nova.galaxy import Connection, Dataset, Parameters, Tool

from nova.galaxy.interfaces import BasicTool



from ips_fastran_gui.app.models.main_model import MainModel
@@ -17,26 +17,36 @@ logger.setLevel(logging.INFO) 
class IPSFastranTool(BasicTool):

    """Class that prepares IPS Fastran tool."""



    def __init__(self, model: MainModel) -> None:

    def __init__(self, model: MainModel, store_factory: Callable, galaxy_url: str, galaxy_api_key: str) -> None:

        super().__init__()

        self.model = model



        connection = Connection(galaxy_url, galaxy_api_key).connect()

        self.store = connection.get_data_store("ips_fastran")



    def prepare_tool(self) -> Tuple[Tool, Parameters]:

        # Prepare file ingestion into Galaxy

        self.inputs_dataset = Dataset(name="inputs.zip")

        with zipfile.ZipFile("input.zip", "w") as zip_obj:

            for file in self.model.config.input_files:

                zip_obj.writestr(file["name"], file["content"].encode("latin1"))

        self.inputs_dataset.path = "input.zip"

        self.config_dataset = Dataset(name="config.txt")

        self.config_dataset.set_content(self.model.config.file_contents)



        # Create the tool instance

        tool_params = Parameters()

        tool_params.add_input(name="inputs", value=self.inputs_dataset)

        tool_params.add_input(name="config", value=self.config_dataset)

        tool_params.add_input(name="shot_number", value=self.model.config.shot_number)

        tool_params.add_input(name="time_id", value=self.model.config.time_id)

        tool_params.add_input(name="__job_resource|__job_resource__select", value="yes")

        tool_params.add_input(name="__job_resource|nodes", value=self.model.resource_params.number_of_nodes)

        tool_params.add_input(name="__job_resource|ntasks_per_node", value=self.model.resource_params.tasks_per_node)

        tool_params.add_input(name="__job_resource|qos", value=self.model.resource_params.partition)

        tool_params.add_input(name="__job_resource|time", value=self.model.resource_params.time_limit)

        tool_params.add_input(name="__job_resource|remote_resource_cloud_nersc", value="nersc")

        self.tool = Tool(id="fusion_ips_fastran")

        self.tool = Tool(id="fusion-ips-fastran")



        return self.tool, tool_params

src/ips_fastran_gui/app/models/main_model.py

+11 −0
Original line number Diff line number Diff line
@@ -20,6 +20,7 @@ class Config(BaseModel): 
    other interfaces for improved clarity and usability.

    """



    input_files: List[Dict[str, Any]] = Field(default=[], title="Input Files")

    shot_number: str = Field(default="000001", title="Shot Number")

    time_id: str = Field(default="00001", title="Time ID")

    file_contents: str = Field(default="")
@@ -33,6 +34,7 @@ class ResourceParameters(BaseModel): 
    partition: str = Field(default="debug", title="Partition")

    number_of_nodes: int = Field(default=1, ge=1, le=2, title="Number of Nodes")

    time_limit: int = Field(default=10, ge=1, le=10080, title="Time Limit (minutes)")

    tasks_per_node: int = Field(default=1, ge=0, le=128, title="Number of Tasks Per Node (0 to disable)")





class PlotJSON(BaseModel):
@@ -55,6 +57,15 @@ class MainModel: 
    def set_config(self, json_data: str) -> None:

        self.config.file_contents = json_data



    def set_files(self, files: List[Dict[str, Any]]) -> None:

        if not files:

            self.config.input_files = []



        for file in files:

            decoded_file = file.copy()

            decoded_file["content"] = decoded_file["content"].decode("latin1")

            self.config.input_files.append(decoded_file)



    def set_plot(self, json_data: str) -> None:

        self.plot_json = PlotJSON.model_validate_json(json_data)

src/ips_fastran_gui/app/view_models/execution.py

+1 −1
Original line number Diff line number Diff line
@@ -29,7 +29,7 @@ class ExecutionViewModel: 
    def __init__(self, model: MainModel, _binding: BindingInterface):

        self.model = model

        galaxy_url, galaxy_api_key = parse_args()

        self.tool = IPSFastranTool(model)

        self.tool = IPSFastranTool(model, self.store_factory, galaxy_url, galaxy_api_key)

        self.tool_runner = ToolRunner("ips_fastran", self.tool, self.store_factory, galaxy_url, galaxy_api_key)

        self.tool_runner.progress_signal.connect(self.on_progress)

        self.completion_signal = signal("ips_fastran_complete")