mseep-rmcp 0.3.3__py3-none-any.whl

rmcp/tools/visualization.py

@@ -0,0 +1,590 @@
+"""
+Visualization tools for RMCP.
+
+Statistical plotting and data visualization capabilities.
+"""
+
+from typing import Dict, Any
+from ..registries.tools import tool
+from ..core.schemas import table_schema, formula_schema
+from ..r_integration import execute_r_script
+
+
+@tool(
+    name="scatter_plot",
+    input_schema={
+        "type": "object",
+        "properties": {
+            "data": table_schema(),
+            "x": {"type": "string"},
+            "y": {"type": "string"},
+            "group": {"type": "string"},
+            "title": {"type": "string"},
+            "file_path": {"type": "string"},
+            "width": {"type": "integer", "minimum": 100, "default": 800},
+            "height": {"type": "integer", "minimum": 100, "default": 600}
+        },
+        "required": ["data", "x", "y", "file_path"]
+    },
+    description="Create scatter plot with optional grouping and trend lines"
+)
+async def scatter_plot(context, params):
+    """Create scatter plot."""
+    
+    await context.info("Creating scatter plot")
+    
+    r_script = '''
+    if (!require(ggplot2)) install.packages("ggplot2", quietly = TRUE)
+    library(ggplot2)
+    
+    data <- as.data.frame(args$data)
+    x_var <- args$x
+    y_var <- args$y
+    group_var <- args$group
+    title <- args$title %||% paste("Scatter plot:", y_var, "vs", x_var)
+    file_path <- args$file_path
+    width <- args$width %||% 800
+    height <- args$height %||% 600
+    
+    # Create base plot
+    p <- ggplot(data, aes_string(x = x_var, y = y_var))
+    
+    if (!is.null(group_var)) {
+        p <- p + geom_point(aes_string(color = group_var), alpha = 0.7) +
+             geom_smooth(aes_string(color = group_var), method = "lm", se = TRUE)
+    } else {
+        p <- p + geom_point(alpha = 0.7) +
+             geom_smooth(method = "lm", se = TRUE, color = "blue")
+    }
+    
+    p <- p + labs(title = title, x = x_var, y = y_var) +
+         theme_minimal() +
+         theme(plot.title = element_text(hjust = 0.5))
+    
+    # Save plot
+    ggsave(file_path, plot = p, width = width/100, height = height/100, dpi = 100)
+    
+    # Basic correlation
+    correlation <- cor(data[[x_var]], data[[y_var]], use = "complete.obs")
+    
+    result <- list(
+        file_path = file_path,
+        x_variable = x_var,
+        y_variable = y_var,
+        group_variable = group_var,
+        correlation = correlation,
+        title = title,
+        n_points = sum(!is.na(data[[x_var]]) & !is.na(data[[y_var]])),
+        plot_saved = file.exists(file_path)
+    )
+    '''
+    
+    try:
+        result = execute_r_script(r_script, params)
+        await context.info("Scatter plot created successfully")
+        return result
+        
+    except Exception as e:
+        await context.error("Scatter plot creation failed", error=str(e))
+        raise
+
+
+@tool(
+    name="histogram",
+    input_schema={
+        "type": "object",
+        "properties": {
+            "data": table_schema(),
+            "variable": {"type": "string"},
+            "group": {"type": "string"},
+            "bins": {"type": "integer", "minimum": 5, "maximum": 100, "default": 30},
+            "title": {"type": "string"},
+            "file_path": {"type": "string"},
+            "width": {"type": "integer", "minimum": 100, "default": 800},
+            "height": {"type": "integer", "minimum": 100, "default": 600}
+        },
+        "required": ["data", "variable", "file_path"]
+    },
+    description="Create histogram with optional grouping and density overlay"
+)
+async def histogram(context, params):
+    """Create histogram."""
+    
+    await context.info("Creating histogram")
+    
+    r_script = '''
+    if (!require(ggplot2)) install.packages("ggplot2", quietly = TRUE)
+    library(ggplot2)
+    
+    data <- as.data.frame(args$data)
+    variable <- args$variable
+    group_var <- args$group
+    bins <- args$bins %||% 30
+    title <- args$title %||% paste("Histogram of", variable)
+    file_path <- args$file_path
+    width <- args$width %||% 800
+    height <- args$height %||% 600
+    
+    # Create base plot
+    p <- ggplot(data, aes_string(x = variable))
+    
+    if (!is.null(group_var)) {
+        p <- p + geom_histogram(aes_string(fill = group_var), bins = bins, alpha = 0.7, position = "identity") +
+             geom_density(aes_string(color = group_var), alpha = 0.8)
+    } else {
+        p <- p + geom_histogram(bins = bins, alpha = 0.7, fill = "steelblue") +
+             geom_density(alpha = 0.8, color = "red")
+    }
+    
+    p <- p + labs(title = title, x = variable, y = "Frequency") +
+         theme_minimal() +
+         theme(plot.title = element_text(hjust = 0.5))
+    
+    # Save plot
+    ggsave(file_path, plot = p, width = width/100, height = height/100, dpi = 100)
+    
+    # Basic statistics
+    values <- data[[variable]][!is.na(data[[variable]])]
+    stats <- list(
+        mean = mean(values),
+        median = median(values),
+        sd = sd(values),
+        skewness = (sum((values - mean(values))^3) / length(values)) / (sd(values)^3),
+        kurtosis = (sum((values - mean(values))^4) / length(values)) / (sd(values)^4) - 3
+    )
+    
+    result <- list(
+        file_path = file_path,
+        variable = variable,
+        group_variable = group_var,
+        bins = bins,
+        statistics = stats,
+        title = title,
+        n_obs = length(values),
+        plot_saved = file.exists(file_path)
+    )
+    '''
+    
+    try:
+        result = execute_r_script(r_script, params)
+        await context.info("Histogram created successfully")
+        return result
+        
+    except Exception as e:
+        await context.error("Histogram creation failed", error=str(e))
+        raise
+
+
+@tool(
+    name="boxplot",
+    input_schema={
+        "type": "object",
+        "properties": {
+            "data": table_schema(),
+            "variable": {"type": "string"},
+            "group": {"type": "string"},
+            "title": {"type": "string"},
+            "file_path": {"type": "string"},
+            "width": {"type": "integer", "minimum": 100, "default": 800},
+            "height": {"type": "integer", "minimum": 100, "default": 600}
+        },
+        "required": ["data", "variable", "file_path"]
+    },
+    description="Create box plot with optional grouping"
+)
+async def boxplot(context, params):
+    """Create box plot."""
+    
+    await context.info("Creating box plot")
+    
+    r_script = '''
+    if (!require(ggplot2)) install.packages("ggplot2", quietly = TRUE)
+    library(ggplot2)
+    
+    data <- as.data.frame(args$data)
+    variable <- args$variable
+    group_var <- args$group
+    title <- args$title %||% paste("Box plot of", variable)
+    file_path <- args$file_path
+    width <- args$width %||% 800
+    height <- args$height %||% 600
+    
+    # Create plot
+    if (!is.null(group_var)) {
+        p <- ggplot(data, aes_string(x = group_var, y = variable, fill = group_var)) +
+             geom_boxplot(alpha = 0.7) +
+             geom_jitter(width = 0.2, alpha = 0.5) +
+             labs(title = title, x = group_var, y = variable)
+    } else {
+        p <- ggplot(data, aes_string(y = variable)) +
+             geom_boxplot(fill = "steelblue", alpha = 0.7) +
+             geom_jitter(width = 0.1, alpha = 0.5) +
+             labs(title = title, x = "", y = variable)
+    }
+    
+    p <- p + theme_minimal() +
+         theme(plot.title = element_text(hjust = 0.5))
+    
+    # Save plot
+    ggsave(file_path, plot = p, width = width/100, height = height/100, dpi = 100)
+    
+    # Summary statistics
+    if (!is.null(group_var)) {
+        stats <- by(data[[variable]], data[[group_var]], function(x) {
+            x_clean <- x[!is.na(x)]
+            list(
+                median = median(x_clean),
+                q1 = quantile(x_clean, 0.25),
+                q3 = quantile(x_clean, 0.75),
+                iqr = IQR(x_clean),
+                n = length(x_clean),
+                outliers = length(boxplot.stats(x_clean)$out)
+            )
+        })
+        summary_stats <- lapply(stats, identity)
+    } else {
+        x_clean <- data[[variable]][!is.na(data[[variable]])]
+        summary_stats <- list(
+            overall = list(
+                median = median(x_clean),
+                q1 = quantile(x_clean, 0.25),
+                q3 = quantile(x_clean, 0.75),
+                iqr = IQR(x_clean),
+                n = length(x_clean),
+                outliers = length(boxplot.stats(x_clean)$out)
+            )
+        )
+    }
+    
+    result <- list(
+        file_path = file_path,
+        variable = variable,
+        group_variable = group_var,
+        summary_statistics = summary_stats,
+        title = title,
+        plot_saved = file.exists(file_path)
+    )
+    '''
+    
+    try:
+        result = execute_r_script(r_script, params)
+        await context.info("Box plot created successfully")
+        return result
+        
+    except Exception as e:
+        await context.error("Box plot creation failed", error=str(e))
+        raise
+
+
+@tool(
+    name="time_series_plot",
+    input_schema={
+        "type": "object",
+        "properties": {
+            "data": {
+                "type": "object",
+                "properties": {
+                    "values": {"type": "array", "items": {"type": "number"}},
+                    "dates": {"type": "array", "items": {"type": "string"}}
+                },
+                "required": ["values"]
+            },
+            "title": {"type": "string"},
+            "file_path": {"type": "string"},
+            "show_trend": {"type": "boolean", "default": True},
+            "width": {"type": "integer", "minimum": 100, "default": 1000},
+            "height": {"type": "integer", "minimum": 100, "default": 600}
+        },
+        "required": ["data", "file_path"]
+    },
+    description="Create time series plot with optional trend line"
+)
+async def time_series_plot(context, params):
+    """Create time series plot."""
+    
+    await context.info("Creating time series plot")
+    
+    r_script = '''
+    if (!require(ggplot2)) install.packages("ggplot2", quietly = TRUE)
+    library(ggplot2)
+    
+    values <- args$data$values
+    dates <- args$data$dates
+    title <- args$title %||% "Time Series Plot"
+    file_path <- args$file_path
+    show_trend <- args$show_trend %||% TRUE
+    width <- args$width %||% 1000
+    height <- args$height %||% 600
+    
+    # Create time index if dates not provided
+    if (is.null(dates)) {
+        time_index <- 1:length(values)
+        x_label <- "Time Index"
+    } else {
+        time_index <- as.Date(dates)
+        x_label <- "Date"
+    }
+    
+    # Create data frame
+    ts_data <- data.frame(
+        time = time_index,
+        value = values
+    )
+    
+    # Create plot
+    p <- ggplot(ts_data, aes(x = time, y = value)) +
+         geom_line(color = "steelblue", size = 1) +
+         geom_point(alpha = 0.6, size = 1.5)
+    
+    if (show_trend) {
+        p <- p + geom_smooth(method = "loess", se = TRUE, color = "red", alpha = 0.3)
+    }
+    
+    p <- p + labs(title = title, x = x_label, y = "Value") +
+         theme_minimal() +
+         theme(plot.title = element_text(hjust = 0.5))
+    
+    # Save plot
+    ggsave(file_path, plot = p, width = width/100, height = height/100, dpi = 100)
+    
+    # Basic time series statistics
+    ts_stats <- list(
+        mean = mean(values, na.rm = TRUE),
+        sd = sd(values, na.rm = TRUE),
+        min = min(values, na.rm = TRUE),
+        max = max(values, na.rm = TRUE),
+        n_obs = length(values[!is.na(values)]),
+        range = max(values, na.rm = TRUE) - min(values, na.rm = TRUE)
+    )
+    
+    result <- list(
+        file_path = file_path,
+        title = title,
+        statistics = ts_stats,
+        has_dates = !is.null(dates),
+        show_trend = show_trend,
+        plot_saved = file.exists(file_path)
+    )
+    '''
+    
+    try:
+        result = execute_r_script(r_script, params)
+        await context.info("Time series plot created successfully")
+        return result
+        
+    except Exception as e:
+        await context.error("Time series plot creation failed", error=str(e))
+        raise
+
+
+@tool(
+    name="correlation_heatmap",
+    input_schema={
+        "type": "object",
+        "properties": {
+            "data": table_schema(),
+            "variables": {"type": "array", "items": {"type": "string"}},
+            "method": {"type": "string", "enum": ["pearson", "spearman", "kendall"], "default": "pearson"},
+            "title": {"type": "string"},
+            "file_path": {"type": "string"},
+            "width": {"type": "integer", "minimum": 100, "default": 800},
+            "height": {"type": "integer", "minimum": 100, "default": 800}
+        },
+        "required": ["data", "file_path"]
+    },
+    description="Create correlation heatmap matrix"
+)
+async def correlation_heatmap(context, params):
+    """Create correlation heatmap."""
+    
+    await context.info("Creating correlation heatmap")
+    
+    r_script = '''
+    if (!require(ggplot2)) install.packages("ggplot2", quietly = TRUE)
+    if (!require(reshape2)) install.packages("reshape2", quietly = TRUE)
+    library(ggplot2)
+    library(reshape2)
+    
+    data <- as.data.frame(args$data)
+    variables <- args$variables
+    method <- args$method %||% "pearson"
+    title <- args$title %||% paste("Correlation Heatmap (", method, ")")
+    file_path <- args$file_path
+    width <- args$width %||% 800
+    height <- args$height %||% 800
+    
+    # Select variables
+    if (is.null(variables)) {
+        numeric_vars <- names(data)[sapply(data, is.numeric)]
+        if (length(numeric_vars) == 0) {
+            stop("No numeric variables found")
+        }
+        variables <- numeric_vars
+    }
+    
+    # Calculate correlation matrix
+    cor_data <- data[, variables, drop = FALSE]
+    cor_matrix <- cor(cor_data, use = "complete.obs", method = method)
+    
+    # Melt for ggplot
+    cor_melted <- melt(cor_matrix)
+    colnames(cor_melted) <- c("Var1", "Var2", "value")
+    
+    # Create heatmap
+    p <- ggplot(cor_melted, aes(Var1, Var2, fill = value)) +
+         geom_tile(color = "white") +
+         scale_fill_gradient2(low = "blue", high = "red", mid = "white", 
+                             midpoint = 0, limit = c(-1, 1), space = "Lab",
+                             name = "Correlation") +
+         theme_minimal() +
+         theme(axis.text.x = element_text(angle = 45, vjust = 1, size = 12, hjust = 1),
+               plot.title = element_text(hjust = 0.5)) +
+         coord_fixed() +
+         labs(title = title, x = "", y = "") +
+         geom_text(aes(label = round(value, 2)), color = "black", size = 3)
+    
+    # Save plot
+    ggsave(file_path, plot = p, width = width/100, height = height/100, dpi = 100)
+    
+    result <- list(
+        file_path = file_path,
+        correlation_matrix = as.matrix(cor_matrix),
+        variables = variables,
+        method = method,
+        title = title,
+        n_variables = length(variables),
+        plot_saved = file.exists(file_path)
+    )
+    '''
+    
+    try:
+        result = execute_r_script(r_script, params)
+        await context.info("Correlation heatmap created successfully")
+        return result
+        
+    except Exception as e:
+        await context.error("Correlation heatmap creation failed", error=str(e))
+        raise
+
+
+@tool(
+    name="regression_plot",
+    input_schema={
+        "type": "object",
+        "properties": {
+            "data": table_schema(),
+            "formula": formula_schema(),
+            "title": {"type": "string"},
+            "file_path": {"type": "string"},
+            "residual_plots": {"type": "boolean", "default": True},
+            "width": {"type": "integer", "minimum": 100, "default": 1200},
+            "height": {"type": "integer", "minimum": 100, "default": 800}
+        },
+        "required": ["data", "formula", "file_path"]
+    },
+    description="Create regression diagnostic plots (fitted vs residuals, Q-Q plot, etc.)"
+)
+async def regression_plot(context, params):
+    """Create regression diagnostic plots."""
+    
+    await context.info("Creating regression plots")
+    
+    r_script = '''
+    if (!require(ggplot2)) install.packages("ggplot2", quietly = TRUE)
+    if (!require(gridExtra)) install.packages("gridExtra", quietly = TRUE)
+    library(ggplot2)
+    library(gridExtra)
+    
+    data <- as.data.frame(args$data)
+    formula <- as.formula(args$formula)
+    title <- args$title %||% "Regression Diagnostics"
+    file_path <- args$file_path
+    residual_plots <- args$residual_plots %||% TRUE
+    width <- args$width %||% 1200
+    height <- args$height %||% 800
+    
+    # Fit model
+    model <- lm(formula, data = data)
+    
+    # Extract model data
+    fitted_values <- fitted(model)
+    residuals <- residuals(model)
+    standardized_residuals <- rstandard(model)
+    
+    if (residual_plots) {
+        # Create diagnostic plots
+        p1 <- ggplot(data.frame(fitted = fitted_values, residuals = residuals), 
+                     aes(x = fitted, y = residuals)) +
+              geom_point(alpha = 0.6) +
+              geom_hline(yintercept = 0, color = "red", linetype = "dashed") +
+              geom_smooth(se = FALSE, color = "blue") +
+              labs(title = "Residuals vs Fitted", x = "Fitted Values", y = "Residuals") +
+              theme_minimal()
+        
+        p2 <- ggplot(data.frame(residuals = standardized_residuals), aes(sample = residuals)) +
+              stat_qq() + stat_qq_line(color = "red") +
+              labs(title = "Q-Q Plot", x = "Theoretical Quantiles", y = "Sample Quantiles") +
+              theme_minimal()
+        
+        p3 <- ggplot(data.frame(fitted = fitted_values, sqrt_abs_residuals = sqrt(abs(standardized_residuals))), 
+                     aes(x = fitted, y = sqrt_abs_residuals)) +
+              geom_point(alpha = 0.6) +
+              geom_smooth(se = FALSE, color = "red") +
+              labs(title = "Scale-Location", x = "Fitted Values", y = "√|Standardized Residuals|") +
+              theme_minimal()
+        
+        p4 <- ggplot(data.frame(leverage = hatvalues(model), std_residuals = standardized_residuals), 
+                     aes(x = leverage, y = std_residuals)) +
+              geom_point(alpha = 0.6) +
+              geom_hline(yintercept = 0, color = "red", linetype = "dashed") +
+              geom_smooth(se = FALSE, color = "blue") +
+              labs(title = "Residuals vs Leverage", x = "Leverage", y = "Standardized Residuals") +
+              theme_minimal()
+        
+        # Combine plots
+        combined_plot <- grid.arrange(p1, p2, p3, p4, ncol = 2, 
+                                     top = textGrob(title, gp = gpar(fontsize = 16, font = 2)))
+        
+        # Save combined plot
+        ggsave(file_path, plot = combined_plot, width = width/100, height = height/100, dpi = 100)
+        
+    } else {
+        # Simple fitted vs actual plot
+        response_var <- all.vars(formula)[1]
+        actual_values <- data[[response_var]]
+        
+        p <- ggplot(data.frame(actual = actual_values, fitted = fitted_values), 
+                   aes(x = actual, y = fitted)) +
+             geom_point(alpha = 0.6) +
+             geom_abline(intercept = 0, slope = 1, color = "red", linetype = "dashed") +
+             labs(title = title, x = "Actual Values", y = "Fitted Values") +
+             theme_minimal() +
+             theme(plot.title = element_text(hjust = 0.5))
+        
+        ggsave(file_path, plot = p, width = width/100, height = height/100, dpi = 100)
+    }
+    
+    # Model summary
+    model_summary <- summary(model)
+    
+    result <- list(
+        file_path = file_path,
+        title = title,
+        r_squared = model_summary$r.squared,
+        adj_r_squared = model_summary$adj.r.squared,
+        residual_se = model_summary$sigma,
+        formula = deparse(formula),
+        residual_plots = residual_plots,
+        n_obs = nobs(model),
+        plot_saved = file.exists(file_path)
+    )
+    '''
+    
+    try:
+        result = execute_r_script(r_script, params)
+        await context.info("Regression plots created successfully")
+        return result
+        
+    except Exception as e:
+        await context.error("Regression plot creation failed", error=str(e))
+        raise

rmcp/transport/__init__.py

@@ -0,0 +1,16 @@
+"""
+Transport layer for MCP server.
+
+Implements transport-agnostic message handling:
+- stdio transport (JSON-RPC over stdin/stdout) 
+- Optional HTTP transport with streaming support
+- Clean separation from business logic
+
+Following the principle: "Business logic never cares whether messages arrive over stdio or HTTP."
+"""
+
+from .stdio import StdioTransport
+from .jsonrpc import JSONRPCEnvelope, JSONRPCError
+from .base import Transport
+
+__all__ = ["StdioTransport", "JSONRPCEnvelope", "JSONRPCError", "Transport"]