Add plugin entrypoints for toolong

See Textualize/toolong#47

Author: ewels

nf_core/toolong_formatter.py

@@ -0,0 +1,203 @@
+from __future__ import annotations
+
+import re
+from datetime import datetime
+from typing import Optional
+
+from rich.text import Text
+from toolong import timestamps
+from toolong.highlighter import LogHighlighter
+from typing_extensions import TypeAlias
+
+ParseResult: TypeAlias = "tuple[Optional[datetime], str, Text]"
+
+
+class LogFormat:
+    def parse(self, line: str) -> ParseResult | None:
+        raise NotImplementedError()
+
+
+class NextflowRegexLogFormatOne(LogFormat):
+    REGEX = re.compile(".*?")
+    LOG_LEVELS = {
+        "DEBUG": ["dim white on black", ""],
+        "INFO": ["bold black on green", "on #042C07"],
+        "WARN": ["bold black on yellow", "on #44450E"],
+        "ERROR": ["bold black on red", "on #470005"],
+    }
+
+    highlighter = LogHighlighter()
+
+    def parse(self, line: str) -> ParseResult | None:
+        match = self.REGEX.fullmatch(line)
+        if match is None:
+            return None
+
+        text = Text.from_ansi(line)
+        groups = match.groupdict()
+        if date := groups.get("date", None):
+            _, timestamp = timestamps.parse(groups["date"])
+            text.highlight_words([date], "not bold magenta")
+        if thread := groups.get("thread", None):
+            text.highlight_words([thread], "blue")
+        if log_level := groups.get("log_level", None):
+            text.highlight_words([f" {log_level} "], self.LOG_LEVELS[log_level][0])
+            text.stylize_before(self.LOG_LEVELS[log_level][1])
+        if logger_name := groups.get("logger_name", None):
+            text.highlight_words([logger_name], "cyan")
+        if process_name := groups.get("process_name", None):
+            text.highlight_words([process_name], "bold cyan")
+        if message := groups.get("message", None):
+            text.highlight_words([message], "dim" if log_level == "DEBUG" else "")
+
+        return None, line, text
+
+
+class NextflowRegexLogFormatTwo(LogFormat):
+    REGEX = re.compile(".*?")
+    highlighter = LogHighlighter()
+
+    def parse(self, line: str) -> ParseResult | None:
+        match = self.REGEX.fullmatch(line)
+        if match is None:
+            return None
+
+        text = Text.from_ansi(line)
+        text.stylize_before("dim")
+        groups = match.groupdict()
+        if process := groups.get("process", None):
+            text.highlight_words([process], "blue not dim")
+        if process_name := groups.get("process_name", None):
+            text.highlight_words([process_name], "bold cyan not dim")
+
+        return None, line, text
+
+
+class NextflowRegexLogFormatThree(LogFormat):
+    REGEX = re.compile(".*?")
+    CHANNEL_TYPES = {
+        "(value)": "green",
+        "(cntrl)": "yellow",
+        "(queue)": "magenta",
+    }
+    highlighter = LogHighlighter()
+
+    def parse(self, line: str) -> ParseResult | None:
+        match = self.REGEX.fullmatch(line)
+        if match is None:
+            return None
+
+        text = Text.from_ansi(line)
+        groups = match.groupdict()
+        if port := groups.get("port", None):
+            text.highlight_words([port], "blue")
+        if channel_type := groups.get("channel_type", None):
+            text.highlight_words([channel_type], self.CHANNEL_TYPES[channel_type])
+        if channel_state := groups.get("channel_state", None):
+            text.highlight_words([channel_state], "cyan" if channel_state == "OPEN" else "yellow")
+        text.highlight_words(["; channel:"], "dim")
+        if channel_name := groups.get("channel_name", None):
+            text.highlight_words([channel_name], "cyan")
+
+        return None, line, text
+
+
+class NextflowRegexLogFormatFour(LogFormat):
+    REGEX = re.compile(".*?")
+    highlighter = LogHighlighter()
+
+    def parse(self, line: str) -> ParseResult | None:
+        match = self.REGEX.fullmatch(line)
+        if match is None:
+            return None
+
+        text = Text.from_ansi(line)
+        text.stylize_before("dim")
+        groups = match.groupdict()
+        text.highlight_words(["status="], "dim")
+        if status := groups.get("status", None):
+            text.highlight_words([status], "cyan not dim")
+
+        return None, line, text
+
+
+class NextflowRegexLogFormatFive(LogFormat):
+    REGEX = re.compile(".*?")
+    highlighter = LogHighlighter()
+
+    def parse(self, line: str) -> ParseResult | None:
+        match = self.REGEX.fullmatch(line)
+        if match is None:
+            return None
+
+        text = Text.from_ansi(line)
+        text.stylize_before("dim")
+        groups = match.groupdict()
+        if script_id := groups.get("script_id", None):
+            text.highlight_words([script_id], "blue")
+        if script_path := groups.get("script_path", None):
+            text.highlight_words([script_path], "magenta")
+
+        return None, line, text
+
+
+class NextflowLogFormat(NextflowRegexLogFormatOne):
+    REGEX = re.compile(
+        r"(?P<date>\w+-\d{2} \d{2}:\d{2}:\d{2}\.\d{3}) (?P<thread>\[.*\]?) (?P<log_level>\w+)\s+(?P<logger_name>[\w\.]+) - (?P<message>.*?)$"
+    )
+
+
+class NextflowLogFormatActiveProcess(NextflowRegexLogFormatTwo):
+    REGEX = re.compile(r"^(?P<marker>\[process\]) (?P<process>.*?)(?P<process_name>[^:]+?)?$")
+
+
+class NextflowLogFormatActiveProcessDetails(NextflowRegexLogFormatThree):
+    REGEX = re.compile(
+        r"  (?P<port>port \d+): (?P<channel_type>\((value|queue|cntrl)\)) (?P<channel_state>\S+)\s+; channel: (?P<channel_name>.*?)$"
+    )
+
+
+class NextflowLogFormatActiveProcessStatus(NextflowRegexLogFormatFour):
+    REGEX = re.compile(r"^  status=(?P<status>.*?)?$")
+
+
+class NextflowLogFormatScriptParse(NextflowRegexLogFormatFive):
+    REGEX = re.compile(r"^  (?P<script_id>Script_\w+:) (?P<script_path>.*?)$")
+
+
+def nextflow_formatters(formats):
+    return [
+        NextflowLogFormat(),
+        NextflowLogFormatActiveProcess(),
+        NextflowLogFormatActiveProcessDetails(),
+        NextflowLogFormatActiveProcessStatus(),
+        NextflowLogFormatScriptParse(),
+    ]
+
+
+def nextflow_format_parser(format_parser):
+    class FormatParser(format_parser):
+        """Parses a log line."""
+
+        def __init__(self) -> None:
+            super().__init__()
+            self._log_status = ""
+
+        def parse(self, line: str) -> ParseResult:
+            """Parse a line."""
+
+            for logtype in ["DEBUG", "INFO", "WARN", "ERROR"]:
+                if logtype in line:
+                    self._log_status = logtype
+                    return super().parse(line)
+            text = Text(line)
+            if text.plain == text.markup:
+                if self._log_status == "DEBUG":
+                    text.stylize("dim")
+                if self._log_status == "WARN":
+                    text.stylize("yellow")
+                if self._log_status == "ERROR":
+                    text.stylize("red")
+            return None, line, text
+
+    return FormatParser

setup.py

@@ -34,6 +34,12 @@
     entry_points={
         "console_scripts": ["nf-core=nf_core.__main__:run_nf_core"],
         "refgenie.hooks.post_update": ["nf-core-refgenie=nf_core.refgenie:update_config"],
+        "toolong.application.formats": [
+            "nextflow_formatters = nf_core.toolong_formatter:nextflow_formatters",
+        ],
+        "toolong.application.format_parsers": [
+            "nextflow_format_parser = nf_core.toolong_formatter:nextflow_format_parser",
+        ],
     },
     python_requires=">=3.8, <4",
     install_requires=required,