dasmixer-cli 0.6.0__py3-none-any.whl

dasmixer/cli/commands/project.py

@@ -0,0 +1,94 @@
+"""CLI commands for project management."""
+
+import typer
+from pathlib import Path
+from typing import Annotated
+import asyncio
+from dasmixer.api.project.project import Project
+from dasmixer.api.config import config
+
+app = typer.Typer(help="Create new project")
+
+
+@app.callback(invoke_without_command=True)
+def create_project(
+    ctx: typer.Context,
+    project_path: Annotated[
+        str,
+        typer.Argument(help="Path to .dasmix project file to create"),
+    ],
+):
+    """
+    Create new empty project with default Control group.
+    """
+    path = Path(project_path)
+
+    # Check if file exists
+    if path.exists():
+        if not typer.confirm(f"File {path} exists. Overwrite?"):
+            typer.echo("Cancelled")
+            raise typer.Exit(0)
+        path.unlink()
+
+    # Create project
+    async def _create():
+        async with Project(path=path, create_if_not_exists=True) as project:
+            await project.add_subset(
+                "Control",
+                details="Default control group",
+                display_color="#3B82F6",
+            )
+            typer.echo(f"✓ Created project: {path}")
+            typer.echo("✓ Added default group: Control")
+
+    try:
+        asyncio.run(_create())
+        config.add_recent_project(str(path))
+    except Exception as e:
+        typer.echo(f"Error creating project: {e}", err=True)
+        raise typer.Exit(1)
+
+
+@app.command()
+def configure(
+    project_path: Annotated[str, typer.Argument(help="Path to .dasmix project file")],
+    key: Annotated[str, typer.Option("--key", "-k", help="Setting key")] = None,
+    value: Annotated[str, typer.Option("--value", "-v", help="Setting value")] = None,
+    list_settings: Annotated[bool, typer.Option("--list", "-l", help="List all settings")] = False,
+):
+    """
+    Configure project settings.
+    """
+    path = Path(project_path)
+    if not path.exists():
+        typer.echo(f"Error: Project file not found: {path}", err=True)
+        raise typer.Exit(1)
+
+    async def _run():
+        async with Project(path=path, create_if_not_exists=False) as project:
+            if list_settings:
+                rows = await project.execute_query(
+                    "SELECT key, value FROM project_settings ORDER BY key"
+                )
+                if not rows:
+                    typer.echo("No settings configured.")
+                    return
+                typer.echo(f"{'Key':<35} {'Value'}")
+                typer.echo("-" * 70)
+                for row in rows:
+                    typer.echo(f"{row['key']:<35} {row['value']}")
+            else:
+                if not key or value is None:
+                    typer.echo("Error: --key and --value are required (or use --list)", err=True)
+                    raise typer.Exit(1)
+                await project.set_setting(key, value)
+                await project.save()
+                typer.echo(f"✓ Setting saved: {key} = {value}")
+
+    try:
+        asyncio.run(_run())
+    except typer.Exit:
+        raise
+    except Exception as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1)

dasmixer/cli/commands/subset.py

@@ -0,0 +1,130 @@
+"""CLI commands for managing comparison groups (subsets)."""
+
+import typer
+from pathlib import Path
+import asyncio
+from dasmixer.api.project.project import Project
+from typing import Annotated
+
+app = typer.Typer(help="Manage comparison groups")
+
+
+@app.command()
+def add(
+    project_path: Annotated[str, typer.Argument(help="Path to .dasmix project file")],
+    name: Annotated[str, typer.Option("--name", "-n", help="Group name")] = ...,
+    details: Annotated[
+        str | None,
+        typer.Option("--details", "-d", help="Group description")
+    ] = None,
+    color: Annotated[
+        str | None,
+        typer.Option("--color", "-c", help="Display color (hex, e.g., #FF5733)")
+    ] = None
+):
+    """Add new comparison group to project."""
+    project_path = Path(project_path)
+    
+    if not project_path.exists():
+        typer.echo(f"Error: Project file not found: {project_path}", err=True)
+        raise typer.Exit(1)
+    
+    async def _add():
+        async with Project(path=project_path, create_if_not_exists=False) as project:
+            subset = await project.add_subset(name, details, color)
+            typer.echo(f"✓ Added group: {subset.name} (id={subset.id})")
+            if details:
+                typer.echo(f"  Description: {details}")
+            if color:
+                typer.echo(f"  Color: {color}")
+    
+    try:
+        asyncio.run(_add())
+    except ValueError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1)
+    except Exception as e:
+        typer.echo(f"Error adding group: {e}", err=True)
+        raise typer.Exit(1)
+
+
+@app.command()
+def delete(
+    project_path: Annotated[str, typer.Argument(help="Path to .dasmix project file")],
+    name: Annotated[str, typer.Option("--name", "-n", help="Group name to delete")] = ...
+):
+    """Delete comparison group from project."""
+    project_path = Path(project_path)
+    
+    if not project_path.exists():
+        typer.echo(f"Error: Project file not found: {project_path}", err=True)
+        raise typer.Exit(1)
+    
+    async def _delete():
+        async with Project(path=project_path, create_if_not_exists=False) as project:
+            # Find subset by name
+            subsets = await project.get_subsets()
+            subset = next((s for s in subsets if s.name == name), None)
+            
+            if not subset:
+                typer.echo(f"Error: Group '{name}' not found", err=True)
+                raise typer.Exit(1)
+            
+            # Confirm deletion
+            if not typer.confirm(f"Delete group '{name}'?"):
+                typer.echo("Cancelled")
+                raise typer.Exit(0)
+            
+            await project.delete_subset(subset.id)
+            typer.echo(f"✓ Deleted group: {name}")
+    
+    try:
+        asyncio.run(_delete())
+    except ValueError as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1)
+    except typer.Exit:
+        raise
+    except Exception as e:
+        typer.echo(f"Error deleting group: {e}", err=True)
+        raise typer.Exit(1)
+
+
+@app.command("list")
+def list_subsets(
+    project_path: Annotated[str, typer.Argument(help="Path to .dasmix project file")]
+):
+    """List all comparison groups in project."""
+    project_path = Path(project_path)
+    
+    if not project_path.exists():
+        typer.echo(f"Error: Project file not found: {project_path}", err=True)
+        raise typer.Exit(1)
+    
+    async def _list():
+        async with Project(path=project_path, create_if_not_exists=False) as project:
+            subsets = await project.get_subsets()
+            
+            if not subsets:
+                typer.echo("No groups found in project")
+                return
+            
+            typer.echo("\nComparison Groups:")
+            typer.echo("=" * 60)
+            
+            for subset in subsets:
+                typer.echo(f"\n{subset.name} (ID: {subset.id})")
+                if subset.details:
+                    typer.echo(f"  Description: {subset.details}")
+                if subset.display_color:
+                    typer.echo(f"  Color: {subset.display_color}")
+                
+                # Count samples in this group
+                samples = await project.get_samples(subset_id=subset.id)
+                typer.echo(f"  Samples: {len(samples)}")
+    
+    try:
+        asyncio.run(_list())
+    except Exception as e:
+        typer.echo(f"Error listing groups: {e}", err=True)
+        raise typer.Exit(1)

dasmixer/cli/commands/tool.py

@@ -0,0 +1,147 @@
+"""CLI commands for managing project tools."""
+
+import json
+import typer
+from pathlib import Path
+from typing import Annotated
+import asyncio
+from dasmixer.api.project.project import Project
+
+app = typer.Typer(help="Manage project tools")
+
+
+@app.command()
+def add(
+    project_path: Annotated[str, typer.Argument(help="Path to .dasmix project file")],
+    name: Annotated[str, typer.Option("--name", "-n", help="Tool name")] = ...,
+    parser: Annotated[str, typer.Option("--parser", "-p", help="Parser name (e.g., PowerNovo2, MGF)")] = ...,
+    type: Annotated[str, typer.Option("--type", "-t", help="Tool type: Library or De Novo")] = "Library",
+    color: Annotated[str, typer.Option("--color", help="Display color (hex, e.g. #4CAF50)")] = None,
+):
+    """
+    Add a new tool to the project.
+    """
+    if type not in ("Library", "De Novo"):
+        typer.echo("Error: --type must be 'Library' or 'De Novo'", err=True)
+        raise typer.Exit(1)
+
+    async def _run():
+        async with Project(path=Path(project_path), create_if_not_exists=False) as project:
+            tools = await project.get_tools()
+            if any(t.name == name for t in tools):
+                typer.echo(f"Error: Tool '{name}' already exists", err=True)
+                raise typer.Exit(1)
+            await project.add_tool(
+                name=name,
+                type=type,
+                parser=parser,
+                settings={},
+                display_color=color,
+            )
+            await project.save()
+            typer.echo(f"✓ Tool added: {name} (parser: {parser}, type: {type})")
+
+    try:
+        asyncio.run(_run())
+    except typer.Exit:
+        raise
+    except Exception as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1)
+
+
+@app.command()
+def configure(
+    project_path: Annotated[str, typer.Argument(help="Path to .dasmix project file")],
+    name: Annotated[str, typer.Option("--name", "-n", help="Tool name")] = ...,
+    key: Annotated[str, typer.Option("--key", "-k", help="Setting key")] = ...,
+    value: Annotated[str, typer.Option("--value", "-v", help="Setting value")] = ...,
+):
+    """
+    Configure a tool setting.
+    """
+    async def _run():
+        async with Project(path=Path(project_path), create_if_not_exists=False) as project:
+            tools = await project.get_tools()
+            tool = next((t for t in tools if t.name == name), None)
+            if not tool:
+                typer.echo(f"Error: Tool '{name}' not found", err=True)
+                raise typer.Exit(1)
+            settings = dict(tool.settings or {})
+            settings[key] = value
+            await project._execute(
+                "UPDATE tool SET settings=? WHERE id=?",
+                [json.dumps(settings), tool.id],
+            )
+            await project.save()
+            typer.echo(f"✓ Tool '{name}' configured: {key} = {value}")
+
+    try:
+        asyncio.run(_run())
+    except typer.Exit:
+        raise
+    except Exception as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1)
+
+
+@app.command(name="param-list")
+def param_list(
+    project_path: Annotated[str, typer.Argument(help="Path to .dasmix project file")],
+    name: Annotated[str, typer.Option("--name", "-n", help="Filter by tool name")] = None,
+):
+    """
+    List tool parameters/settings.
+    """
+    async def _run():
+        async with Project(path=Path(project_path), create_if_not_exists=False) as project:
+            tools = await project.get_tools()
+            if name:
+                tools = [t for t in tools if t.name == name]
+                if not tools:
+                    typer.echo(f"Error: Tool '{name}' not found", err=True)
+                    raise typer.Exit(1)
+            for tool in tools:
+                typer.echo(f"\nTool: {tool.name} ({tool.parser}, {tool.type})")
+                settings = tool.settings or {}
+                if settings:
+                    for k, v in settings.items():
+                        typer.echo(f"  {k:<20} = {v}")
+                else:
+                    typer.echo("  (no settings)")
+
+    try:
+        asyncio.run(_run())
+    except typer.Exit:
+        raise
+    except Exception as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1)
+
+
+@app.command()
+def list(
+    project_path: Annotated[str, typer.Argument(help="Path to .dasmix project file")],
+):
+    """
+    List all tools in the project.
+    """
+    async def _run():
+        async with Project(path=Path(project_path), create_if_not_exists=False) as project:
+            tools = await project.get_tools()
+            if not tools:
+                typer.echo("No tools found.")
+                return
+            typer.echo(f"{'ID':<5} {'Name':<20} {'Type':<12} {'Parser':<20} {'Settings'}")
+            typer.echo("-" * 70)
+            for t in tools:
+                settings_count = len(t.settings or {})
+                typer.echo(f"{t.id:<5} {t.name:<20} {t.type:<12} {t.parser:<20} {settings_count} keys")
+
+    try:
+        asyncio.run(_run())
+    except typer.Exit:
+        raise
+    except Exception as e:
+        typer.echo(f"Error: {e}", err=True)
+        raise typer.Exit(1)

dasmixer/cli/main.py

@@ -0,0 +1,52 @@
+"""
+DASMixer CLI — entry point for the `dasmixer-cli` command.
+
+Provides command-line tools for project management without GUI.
+"""
+
+import typer
+from typing import Annotated
+from pathlib import Path
+
+from dasmixer.versions import APP_VERSION
+from dasmixer.cli.commands import project, subset, import_data
+from dasmixer.cli.commands import portable
+from dasmixer.cli.commands import import_project as import_project_cmd
+from dasmixer.cli.commands import tool as tool_cmd
+from dasmixer.cli.commands import calculate as calculate_cmd
+
+app = typer.Typer(
+    name="dasmixer-cli",
+    help="DASMixer CLI — manage projects without GUI",
+    add_completion=False,
+)
+
+
+@app.callback(invoke_without_command=True)
+def main(
+    ctx: typer.Context,
+    version: Annotated[
+        bool,
+        typer.Option("--version", "-v", help="Show version and exit"),
+    ] = False,
+):
+    """DASMixer CLI — управление проектами без GUI."""
+    if version:
+        typer.echo(f"DASMixer CLI {APP_VERSION}")
+        raise typer.Exit(0)
+    if ctx.invoked_subcommand is None:
+        typer.echo(ctx.get_help())
+
+
+app.add_typer(project.app, name="create", help="Create new project")
+app.add_typer(project.app, name="project", help="Manage project settings (configure)")
+app.add_typer(subset.app, name="subset", help="Manage comparison groups")
+app.add_typer(import_data.app, name="import", help="Import data files")
+app.add_typer(portable.app, name="checkpoint", help="Save WAL to database file")
+app.add_typer(portable.app, name="vacuum", help="Compact database file")
+app.add_typer(import_project_cmd.app, name="import-project", help="Merge another project into this one")
+app.add_typer(tool_cmd.app, name="tool", help="Manage project tools")
+app.add_typer(calculate_cmd.app, name="calculate", help="Run pipeline calculations")
+
+if __name__ == "__main__":
+    app()

dasmixer_cli-0.6.0.dist-info/METADATA

@@ -0,0 +1,51 @@
+Metadata-Version: 2.4
+Name: dasmixer-cli
+Version: 0.6.0
+Summary: DASMixer CLI — command-line tools for project management
+Author: gluck
+Author-email: glucksistemi@gmail.com
+Requires-Python: <4.0, >=3.11
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: dasmixer-core (==0.6.0)
+Project-URL: Homepage, https://github.com/protdb/dasmixer
+Description-Content-Type: text/markdown
+
+# DASMixer CLI
+
+Command-line tools for managing DASMixer projects without a graphical interface.
+
+## Installation
+
+```bash
+pip install dasmixer-cli
+```
+
+## Usage
+
+```bash
+dasmixer-cli --help
+dasmixer-cli create path/to/project.dasmix
+dasmixer-cli subset list path/to/project.dasmix
+dasmixer-cli subset add path/to/project.dasmix --name "Treatment" --color "#FF5733"
+dasmixer-cli import mgf-file path/to/project.dasmix --sample "Sample1" --file spectra.mgf
+dasmixer-cli import mgf-pattern path/to/project.dasmix --sample "Sample1" --folder ./spectra/ --pattern "*.mgf"
+```
+
+## Commands
+
+| Command | Description |
+|---|---|
+| `create <project>` | Create a new empty project |
+| `subset list <project>` | List comparison groups |
+| `subset add <project> --name` | Add a comparison group |
+| `subset delete <project> --name` | Delete a comparison group |
+| `import mgf-file <project>` | Import a single MGF file |
+| `import mgf-pattern <project>` | Batch import MGF files by pattern |
+| `import ident-file <project>` | Import an identification file |
+| `import ident-pattern <project>` | Batch import identification files |
+
+Documentation: https://github.com/protdb/dasmixer

dasmixer_cli-0.6.0.dist-info/RECORD

@@ -0,0 +1,14 @@
+dasmixer/cli/__init__.py,sha256=LAxO9P8FGo1i5-bimxDHP3P9Wskh_Hs1Jf0Oq1Ne2ek,82
+dasmixer/cli/commands/__init__.py,sha256=VGM6t1ow3-15tV5QtnEJov7qjluWtLBRP4tDCvcon_8,78
+dasmixer/cli/commands/calculate.py,sha256=j6vsoo6mA9ngIvQoCc5zl6VKaYbFAz0yLm4mjvXkJz8,23325
+dasmixer/cli/commands/import_data.py,sha256=c67xm_AivuWmHNhPTqPVTwdhs4eKXo3355XHdBNBU2s,19244
+dasmixer/cli/commands/import_project.py,sha256=kDud5tJI6lMP0Xdk5LyfPSCKONWTDhdhWcEASOjYaJ4,2999
+dasmixer/cli/commands/portable.py,sha256=5jcmREk7vHTocV-zgK0ijsIX6nWHWsQhrPj4dRmxklM,1719
+dasmixer/cli/commands/project.py,sha256=4jmZOAFzoZ9MtQt2-wDbkQ5LGh2T2_DtQwwqeyAZ3Cs,3188
+dasmixer/cli/commands/subset.py,sha256=M7uuaUG--HJVQ6fgyQgHCrIdxBAxDYBNO_-X6sDSxrA,4593
+dasmixer/cli/commands/tool.py,sha256=cAO1c7hFpj-bMBS9mYFA3l1CdvResE8Qt6mcQWGXIUY,5324
+dasmixer/cli/main.py,sha256=N8xmhmLpMlmwyiZQ5jriv_ICW7UfpeJDFCtr2tOfuO8,1923
+dasmixer_cli-0.6.0.dist-info/entry_points.txt,sha256=a4KExsoM5TAa1-M7059iMIH3u9VerPOAyCF4mQz-so0,54
+dasmixer_cli-0.6.0.dist-info/METADATA,sha256=gHDykCWY7rhQFGVKzU6IphkSWr3vuSayhCrMcohG0vA,1766
+dasmixer_cli-0.6.0.dist-info/WHEEL,sha256=Vz2fHgx6HFtSwhs8KvkHLqH5Ea4w1_rner5uNVGCeIE,88
+dasmixer_cli-0.6.0.dist-info/RECORD,,

dasmixer_cli-0.6.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: poetry-core 2.3.2
+Root-Is-Purelib: true
+Tag: py3-none-any

dasmixer_cli-0.6.0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+dasmixer-cli=dasmixer.cli.main:app
+