Merge pull request #3008 from mirpedrol/pipeline-name-validation

Create: allow more special characters on the pipeline name for non-nf-core pipelines

CHANGELOG.md

@@ -25,6 +25,7 @@
 - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
 - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006))
+- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

nf_core/pipelines/create/__init__.py

@@ -5,6 +5,7 @@
 from textual.app import App
 from textual.widgets import Button
 
+from nf_core.pipelines.create import utils
 from nf_core.pipelines.create.basicdetails import BasicDetails
 from nf_core.pipelines.create.custompipeline import CustomPipeline
 from nf_core.pipelines.create.finaldetails import FinalDetails
@@ -14,15 +15,10 @@
 from nf_core.pipelines.create.loggingscreen import LoggingScreen
 from nf_core.pipelines.create.nfcorepipeline import NfcorePipeline
 from nf_core.pipelines.create.pipelinetype import ChoosePipelineType
-from nf_core.pipelines.create.utils import (
-    CreateConfig,
-    CustomLogHandler,
-    LoggingConsole,
-)
 from nf_core.pipelines.create.welcome import WelcomeScreen
 
-log_handler = CustomLogHandler(
-    console=LoggingConsole(classes="log_console"),
+log_handler = utils.CustomLogHandler(
+    console=utils.LoggingConsole(classes="log_console"),
     rich_tracebacks=True,
     show_time=False,
     show_path=False,
@@ -36,7 +32,7 @@
 log_handler.setLevel("INFO")
 
 
-class PipelineCreateApp(App[CreateConfig]):
+class PipelineCreateApp(App[utils.CreateConfig]):
     """A Textual app to manage stopwatches."""
 
     CSS_PATH = "create.tcss"
@@ -60,10 +56,10 @@ class PipelineCreateApp(App[CreateConfig]):
     }
 
     # Initialise config as empty
-    TEMPLATE_CONFIG = CreateConfig()
+    TEMPLATE_CONFIG = utils.CreateConfig()
 
     # Initialise pipeline type
-    PIPELINE_TYPE = None
+    NFCORE_PIPELINE = True
 
     # Log handler
     LOG_HANDLER = log_handler
@@ -78,10 +74,12 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
         if event.button.id == "start":
             self.push_screen("choose_type")
         elif event.button.id == "type_nfcore":
-            self.PIPELINE_TYPE = "nfcore"
+            self.NFCORE_PIPELINE = True
+            utils.NFCORE_PIPELINE_GLOBAL = True
             self.push_screen("basic_details")
         elif event.button.id == "type_custom":
-            self.PIPELINE_TYPE = "custom"
+            self.NFCORE_PIPELINE = False
+            utils.NFCORE_PIPELINE_GLOBAL = False
             self.push_screen("basic_details")
         elif event.button.id == "continue":
             self.push_screen("final_details")

nf_core/pipelines/create/basicdetails.py

@@ -39,7 +39,7 @@ def compose(self) -> ComposeResult:
                 "GitHub organisation",
                 "nf-core",
                 classes="column",
-                disabled=self.parent.PIPELINE_TYPE == "nfcore",
+                disabled=self.parent.NFCORE_PIPELINE,
             )
             yield TextInput(
                 "name",
@@ -85,7 +85,7 @@ def on_screen_resume(self):
         add_hide_class(self.parent, "exist_warn")
         for text_input in self.query("TextInput"):
             if text_input.field_id == "org":
-                text_input.disabled = self.parent.PIPELINE_TYPE == "nfcore"
+                text_input.disabled = self.parent.NFCORE_PIPELINE
 
     @on(Button.Pressed)
     def on_button_pressed(self, event: Button.Pressed) -> None:
@@ -102,9 +102,9 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
         try:
             self.parent.TEMPLATE_CONFIG = CreateConfig(**config)
             if event.button.id == "next":
-                if self.parent.PIPELINE_TYPE == "nfcore":
+                if self.parent.NFCORE_PIPELINE:
                     self.parent.push_screen("type_nfcore")
-                elif self.parent.PIPELINE_TYPE == "custom":
+                else:
                     self.parent.push_screen("type_custom")
         except ValueError:
             pass

nf_core/pipelines/create/utils.py

@@ -1,9 +1,11 @@
 import re
+from contextlib import contextmanager
+from contextvars import ContextVar
 from logging import LogRecord
 from pathlib import Path
-from typing import Optional, Union
+from typing import Any, Dict, Iterator, Optional, Union
 
-from pydantic import BaseModel, ConfigDict, ValidationError, field_validator
+from pydantic import BaseModel, ConfigDict, ValidationError, ValidationInfo, field_validator
 from rich.logging import RichHandler
 from textual import on
 from textual._context import active_app
@@ -14,6 +16,22 @@
 from textual.widget import Widget
 from textual.widgets import Button, Input, Markdown, RichLog, Static, Switch
 
+# Use ContextVar to define a context on the model initialization
+_init_context_var: ContextVar = ContextVar("_init_context_var", default={})
+
+
+@contextmanager
+def init_context(value: Dict[str, Any]) -> Iterator[None]:
+    token = _init_context_var.set(value)
+    try:
+        yield
+    finally:
+        _init_context_var.reset(token)
+
+
+# Define a global variable to store the pipeline type
+NFCORE_PIPELINE_GLOBAL: bool = True
+
 
 class CreateConfig(BaseModel):
     """Pydantic model for the nf-core create config."""
@@ -30,12 +48,25 @@ class CreateConfig(BaseModel):
 
     model_config = ConfigDict(extra="allow")
 
+    def __init__(self, /, **data: Any) -> None:
+        """Custom init method to allow using a context on the model initialization."""
+        self.__pydantic_validator__.validate_python(
+            data,
+            self_instance=self,
+            context=_init_context_var.get(),
+        )
+
     @field_validator("name")
     @classmethod
-    def name_nospecialchars(cls, v: str) -> str:
+    def name_nospecialchars(cls, v: str, info: ValidationInfo) -> str:
         """Check that the pipeline name is simple."""
-        if not re.match(r"^[a-z]+$", v):
-            raise ValueError("Must be lowercase without punctuation.")
+        context = info.context
+        if context and context["is_nfcore"]:
+            if not re.match(r"^[a-z]+$", v):
+                raise ValueError("Must be lowercase without punctuation.")
+        else:
+            if not re.match(r"^[a-zA-Z-_]+$", v):
+                raise ValueError("Must not contain special characters. Only '-' or '_' are allowed.")
         return v
 
     @field_validator("org", "description", "author", "version", "outdir")
@@ -117,8 +148,9 @@ def validate(self, value: str) -> ValidationResult:
 
         If it fails, return the error messages."""
         try:
-            CreateConfig(**{f"{self.key}": value})
-            return self.success()
+            with init_context({"is_nfcore": NFCORE_PIPELINE_GLOBAL}):
+                CreateConfig(**{f"{self.key}": value})
+                return self.success()
         except ValidationError as e:
             return self.failure(", ".join([err["msg"] for err in e.errors()]))