WIP: Restructure with components and plugins

Author: kks32

Diff for: dapi/__init__.py

@@ -36,7 +36,11 @@
 ```
 
 """
-from . import apps
-from . import auth
-from . import db
-from . import jobs
+# from . import apps
+# from . import auth
+# from . import db
+# from . import jobs
+
+from .core import DesignSafeAPI
+
+__all__ = ["DesignSafeAPI", "apps", "auth", "db", "jobs", "core"]

Diff for: dapi/components/__init__.py

@@ -0,0 +1 @@
+# components/__init__.py

Diff for: dapi/components/files/__init__.py

@@ -0,0 +1,253 @@
+# designsafe/components/files/__init__.py
+from pathlib import Path
+from typing import Optional, List, Union, Dict
+from enum import Enum
+from dataclasses import dataclass
+import os
+
+from ...core import BaseComponent
+
+
+class StorageSystem(Enum):
+    """Enumeration of DesignSafe storage systems."""
+
+    MY_DATA = "designsafe.storage.default"
+    COMMUNITY_DATA = "designsafe.storage.community"
+
+    @property
+    def base_path(self) -> str:
+        """Get the base Jupyter path for this storage system."""
+        return {
+            StorageSystem.MY_DATA: "jupyter/MyData",
+            StorageSystem.COMMUNITY_DATA: "jupyter/CommunityData",
+        }[self]
+
+
+@dataclass
+class FileInfo:
+    """Information about a file or directory in DesignSafe."""
+
+    name: str
+    path: str
+    type: str  # 'file' or 'dir'
+    size: Optional[int]
+    last_modified: str
+    uri: str
+    permissions: Dict[str, bool]
+
+
+class FilesComponent(BaseComponent):
+    """Component for managing files and directories in DesignSafe."""
+
+    def _get_project_uuid(self, project_id: str) -> str:
+        """Get the UUID for a project given its ID.
+
+        Args:
+            project_id: The project ID
+
+        Returns:
+            The project UUID
+
+        Raises:
+            ValueError: If project not found
+        """
+        try:
+            resp = self.tapis.get(
+                f"https://designsafe-ci.org/api/projects/v2/{project_id}"
+            )
+            project_data = resp.json()
+            return project_data["baseProject"]["uuid"]
+        except Exception as e:
+            raise ValueError(f"Error getting project UUID for {project_id}: {str(e)}")
+
+    def get_uri(self, path: str) -> str:
+        """Convert a local or Jupyter path to a Tapis URI.
+
+        Args:
+            path: Local filesystem or Jupyter path
+
+        Returns:
+            Tapis URI for the path
+
+        Examples:
+            >>> ds.files.get_uri("jupyter/MyData/test.txt")
+            'tapis://designsafe.storage.default/username/test.txt'
+
+            >>> ds.files.get_uri("jupyter/CommunityData/test.txt")
+            'tapis://designsafe.storage.community/test.txt'
+
+            >>> ds.files.get_uri("jupyter/MyProjects/PRJ-1234/test.txt")
+            'tapis://project-uuid/test.txt'
+        """
+        path = str(path)  # Convert Path objects to string
+
+        # Handle MyData paths
+        if "MyData" in path or "mydata" in path:
+            # Extract the relative path after MyData
+            rel_path = path.split("MyData/")[-1]
+            return f"tapis://{StorageSystem.MY_DATA.value}/{self.tapis.username}/{rel_path}"
+
+        # Handle CommunityData paths
+        if "CommunityData" in path:
+            rel_path = path.split("CommunityData/")[-1]
+            return f"tapis://{StorageSystem.COMMUNITY_DATA.value}/{rel_path}"
+
+        # Handle Project paths
+        if "MyProjects" in path or "projects" in path:
+            # Extract project ID and relative path
+            parts = path.split("/")
+            for i, part in enumerate(parts):
+                if part in ("MyProjects", "projects"):
+                    project_id = parts[i + 1]
+                    rel_path = "/".join(parts[i + 2 :])
+                    break
+            else:
+                raise ValueError("Could not parse project path")
+
+            project_uuid = self._get_project_uuid(project_id)
+            return f"tapis://project-{project_uuid}/{rel_path}"
+
+        raise ValueError(f"Could not determine storage system for path: {path}")
+
+    def list(self, path: str, recursive: bool = False) -> List[FileInfo]:
+        """List contents of a directory.
+
+        Args:
+            path: Path to list
+            recursive: Whether to list contents recursively
+
+        Returns:
+            List of FileInfo objects
+
+        Raises:
+            Exception: If listing fails
+        """
+        uri = self.get_uri(path)
+
+        try:
+            system_id, path = uri.replace("tapis://", "").split("/", 1)
+
+            listing = self.tapis.files.listFiles(
+                systemId=system_id, path=path, recursive=recursive
+            )
+
+            return [
+                FileInfo(
+                    name=item.name,
+                    path=item.path,
+                    type="dir" if item.type == "dir" else "file",
+                    size=item.size,
+                    last_modified=item.lastModified,
+                    uri=f"tapis://{system_id}/{item.path}",
+                    permissions={
+                        "read": item.permissions.read,
+                        "write": item.permissions.write,
+                        "execute": item.permissions.execute,
+                    },
+                )
+                for item in listing
+            ]
+        except Exception as e:
+            raise Exception(f"Error listing {path}: {str(e)}")
+
+    def upload(
+        self, local_path: Union[str, Path], remote_path: str, progress: bool = True
+    ) -> FileInfo:
+        """Upload a file or directory to DesignSafe.
+
+        Args:
+            local_path: Path to local file/directory to upload
+            remote_path: Destination path on DesignSafe
+            progress: Whether to show progress bar
+
+        Returns:
+            FileInfo object for the uploaded file
+
+        Raises:
+            FileNotFoundError: If local path doesn't exist
+            Exception: If upload fails
+        """
+        local_path = Path(local_path)
+        if not local_path.exists():
+            raise FileNotFoundError(f"Local path not found: {local_path}")
+
+        uri = self.get_uri(remote_path)
+        system_id, path = uri.replace("tapis://", "").split("/", 1)
+
+        try:
+            result = self.tapis.files.upload(
+                systemId=system_id,
+                sourcePath=str(local_path),
+                targetPath=path,
+                progress=progress,
+            )
+
+            # Return info about the uploaded file
+            return FileInfo(
+                name=local_path.name,
+                path=path,
+                type="dir" if local_path.is_dir() else "file",
+                size=local_path.stat().st_size if local_path.is_file() else None,
+                last_modified=result.lastModified,
+                uri=uri,
+                permissions={"read": True, "write": True, "execute": False},
+            )
+        except Exception as e:
+            raise Exception(f"Error uploading {local_path} to {remote_path}: {str(e)}")
+
+    def download(
+        self,
+        remote_path: str,
+        local_path: Optional[Union[str, Path]] = None,
+        progress: bool = True,
+    ) -> Path:
+        """Download a file or directory from DesignSafe.
+
+        Args:
+            remote_path: Path on DesignSafe to download
+            local_path: Local destination path (default: current directory)
+            progress: Whether to show progress bar
+
+        Returns:
+            Path to downloaded file/directory
+
+        Raises:
+            Exception: If download fails
+        """
+        uri = self.get_uri(remote_path)
+        system_id, path = uri.replace("tapis://", "").split("/", 1)
+
+        # Default to current directory with remote filename
+        if local_path is None:
+            local_path = Path.cwd() / Path(path).name
+        local_path = Path(local_path)
+
+        try:
+            self.tapis.files.download(
+                systemId=system_id,
+                path=path,
+                targetPath=str(local_path),
+                progress=progress,
+            )
+            return local_path
+        except Exception as e:
+            raise Exception(
+                f"Error downloading {remote_path} to {local_path}: {str(e)}"
+            )
+
+    def delete(self, path: str) -> None:
+        """Delete a file or directory.
+
+        Args:
+            path: Path to delete
+
+        Raises:
+            Exception: If deletion fails
+        """
+        uri = self.get_uri(path)
+        system_id, path = uri.replace("tapis://", "").split("/", 1)
+
+        try:
+            self.tapis.files.delete(systemId=system_id, path=path)
+        except Exception as e:
+            raise Exception(f"Error deleting {path}: {str(e)}")

Diff for: dapi/components/jobs/__init__.py

@@ -0,0 +1,107 @@
+from typing import Dict, Type, Any, Optional
+from .base_job_handler import BaseJobHandler
+from ...core import BaseComponent  # Importing BaseComponent from core
+from datetime import datetime
+from tqdm import tqdm
+import time
+
+
+class JobsComponent(BaseComponent):
+    """Jobs component for managing Tapis jobs."""
+
+    def __init__(self, api):
+        super().__init__(api)
+        self.handlers: Dict[str, Type[BaseJobHandler]] = {}
+        self._register_default_handlers()
+
+    def _register_default_handlers(self) -> None:
+        """Register default job handlers."""
+        from .opensees_job_handler import OpenSeesJobHandler  # Import default handlers
+
+        self.register_handler("opensees", OpenSeesJobHandler)
+
+    def register_handler(
+        self, app_name: str, handler_class: Type[BaseJobHandler]
+    ) -> None:
+        """Register a handler for a specific app."""
+        self.handlers[app_name] = handler_class
+
+        # Dynamically add a method for the app
+        def app_method(
+            input_file: str,
+            input_uri: Optional[str] = None,
+            job_name: Optional[str] = None,
+            max_minutes: Optional[int] = None,
+            node_count: Optional[int] = None,
+            cores_per_node: Optional[int] = None,
+            queue: Optional[str] = None,
+            allocation: Optional[str] = None,
+        ) -> Any:
+            handler = self.handlers[app_name](app_name)
+            job_info = handler.generate_job_info(
+                self.tapis,
+                input_uri or "tapis://example/input/",
+                input_file,
+                job_name,
+                max_minutes,
+                node_count,
+                cores_per_node,
+                queue,
+                allocation,
+            )
+            return job_info
+
+        setattr(self, app_name, app_method)
+
+    def submit_job(self, job_info: Dict[str, Any]) -> Any:
+        """Submit a job to Tapis."""
+        response = self.tapis.jobs.submitJob(**job_info)
+        return response
+
+    def monitor_job(self, job_uuid: str, interval: int = 15) -> str:
+        """Monitor the status of a job."""
+        status = self.tapis.jobs.getJobStatus(jobUuid=job_uuid).status
+        max_minutes = self.tapis.jobs.getJob(jobUuid=job_uuid).maxMinutes
+        previous_status = None
+
+        with tqdm(desc="Monitoring Job", dynamic_ncols=True) as pbar:
+            for _ in range(int(max_minutes * 60 / interval)):
+                time.sleep(interval)
+                status = self.tapis.jobs.getJobStatus(jobUuid=job_uuid).status
+                if status != previous_status:
+                    tqdm.write(f"Status changed: {status}")
+                    previous_status = status
+
+                if status in ["FINISHED", "FAILED", "STOPPED"]:
+                    break
+                pbar.update(1)
+
+        return status
+
+    def get_job_history(self, job_uuid: str) -> Dict[str, Any]:
+        """Retrieve job history and compute timings."""
+        history = self.tapis.jobs.getJobHistory(jobUuid=job_uuid)
+        timing_summary = {}
+
+        def parse_timestamps(event_list, event_name):
+            timestamps = [
+                datetime.strptime(event.created, "%Y-%m-%dT%H:%M:%S.%fZ")
+                for event in event_list
+                if event.eventDetail == event_name
+            ]
+            return timestamps
+
+        queued_times = parse_timestamps(history, "QUEUED")
+        running_times = parse_timestamps(history, "RUNNING")
+
+        if queued_times and running_times:
+            timing_summary["QUEUED"] = (
+                running_times[0] - queued_times[0]
+            ).total_seconds()
+
+        if running_times and len(running_times) > 1:
+            timing_summary["RUNNING"] = (
+                running_times[-1] - running_times[0]
+            ).total_seconds()
+
+        return timing_summary